Merge branch 'feature-documentation' into 'release-0.2.0'

merge Feature documentation into release 0.2.0

#38

See merge request !63

docs/general/config.md

+# How to create configs
+
+### The sample config
+
+The sample config should be in [__JSON__](http://www.json.org/) format
+
+- First field should have the key __"samples"__
+- Second field should contain the __"libraries"__
+- Third field contains __"R1" or "R2"__ or __"bam"__
+- The fastq input files can be provided zipped and un zipped
+
+#### Example sample config
+~~~
+    {  
+       "samples":{  
+          "Sample_ID1":{  
+             "libraries":{  
+                "MySeries_1":{  
+                   "R1":"Your_R1.fastq.gz",
+                   "R2":"Your_R2.fastq.gz"
+                }
+             }
+          }
+       }
+    }
+~~~
+
+- For BAM files as input one should use a config like this:
+  
+~~~
+    {
+       "samples":{  
+          "Sample_ID_1":{  
+             "libraries":{  
+                "Lib_ID_1":{  
+                   "bam":"MyFirst.bam"
+                },
+                "Lib_ID_2":{  
+                   "bam":"MySecond.bam"
+                }
+             }
+          }
+       }
+    }
+~~~
+
+
+Note that there is a tool called [SamplesTsvToJson](../tools/SamplesTsvToJson.md) this enables a user to get the sample config without any chance of creating a wrongly formatted JSON file.
+
+
+### The settings config
+The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
+This config file should be written in JSON format. It can contain setup settings like references for the tools used,
+if the pipeline should use chunking or setting memory limits for certain programs almost everything can be adjusted trough this config file.
+One could set global variables containing settings for all tools used in the pipeline or set tool specific options one layer deeper into the JSON file.
+E.g. in the example below the settings for Picard tools are altered only for Picard and not global. 
+
+~~~
+"picard": { "validationstringency": "LENIENT" } 
+~~~
+
+Global setting examples are:
+~~~
+"java_gc_timelimit": 98,
+"numberchunks": 25,
+"chunking": true
+~~~
+
+
+----
+
+#### Example settings config
+~~~
+{
+        "reference": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/ucsc.hg19_nohap.fasta",
+        "dbsnp": "/data/LGTC/projects/vandoorn-melanoma/data/references/hg19_nohap/dbsnp_137.hg19_nohap.vcf",
+        "joint_variantcalling": false,
+        "haplotypecaller": { "scattercount": 100 },
+        "multisample": { "haplotypecaller": { "scattercount": 1000 } },
+        "picard": { "validationstringency": "LENIENT" },
+        "library_variantcalling_temp": true,
+        "target_bed_temp": "/data/LGTC/projects/vandoorn-melanoma/analysis/target.bed",
+        "min_dp": 5,
+        "bedtools": {"exe":"/share/isilon/system/local/BEDtools/bedtools-2.17.0/bin/bedtools"},
+        "bam_to_fastq": true,
+        "baserecalibrator": { "memory_limit": 8, "vmem":"16G" },
+        "samtofastq": {"memory_limit": 8, "vmem": "16G"},
+        "java_gc_timelimit": 98,
+        "numberchunks": 25,
+        "chunking": true,
+        "haplotypecaller": { "scattercount": 1000 }
+}
+~~~
+
+### JSON validation
+
+To check if the JSON file created is correct we can use multiple options the simplest way is using [this](http://jsonformatter.curiousconcept.com/)
+website. It is also possible to use Python or Scala for validating but this requires some more knowledge.
\ No newline at end of file

docs/index.md

@@ -52,7 +52,7 @@ java -jar Biopet(version).jar (pipeline of interest) (pipeline options) -qsub* -
 ~~~
 java -jar Biopet(version).jar (pipeline of interest) (pipeline options) 
 ~~~
-    
+If one performs a dry run the config report will be generated. From this config report you can identify all configurable options.
 
 ### Shark Compute Cluster specific
 
@@ -85,18 +85,14 @@ Using this option, the `java -jar Biopet-<version>.jar` can be ommited and `biop
 - [Sage](pipelines/sage)
 - Yamsvp (Under development)
 
-__Note that each pipeline needs a config file written in JSON format see [config](config.md) & [How To! Config](https://git.lumc.nl/biopet/biopet/wikis/Config) __
+__Note that each pipeline needs a config file written in JSON format see [config](general/config.md) & [How To! Config](https://git.lumc.nl/biopet/biopet/wikis/Config) __
 
 
 There are multiple configs that can be passed to a pipeline, for example the sample, settings and executables wherefrom sample and settings are mandatory.
 
-- [Here](config) one can find how to create a sample and settings config
+- [Here](general/config.md) one can find how to create a sample and settings config
 - More info can be found here: [How To! Config](https://git.lumc.nl/biopet/biopet/wikis/Config)
 
-
-
-
-
 ### Running a tool
 
     $ biopet tool <tool_name>

docs/license.md

+Public release:
+~~~bash
+Biopet is built on top of GATK Queue for building bioinformatic 
+pipelines. It is mainly intended to support LUMC SHARK cluster which is running 
+SGE. But other types of HPC that are supported by GATK Queue (such as PBS) 
+should also be able to execute Biopet tools and pipelines. 
+
+Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+
+Contact us at: sasc@lumc.nl
+
+A dual licensing mode is applied. The source code within this project that are 
+not part of GATK Queue is freely available for non-commercial use under an AGPL 
+license; For commercial users or users who do not want to follow the AGPL 
+license, please contact us to obtain a separate license.
+~~~
+
+Private release:
+~~~bash
+Due to the license issue with GATK, this part of Biopet can only be used inside the 
+LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions 
+on how to use this protected part of biopet or contact us at sasc@lumc.nl
+~~~
+
     Copyright [2013-2014] [Sequence Analysis Support Core](https://sasc.lumc.nl/)

docs/pipelines/GATK-pipeline.md

@@ -28,7 +28,7 @@ The pipeline accepts ```.fastq & .bam``` files as input.
 
 ## Example
 
-Note that one should first create the appropriate [configs](../config.md).
+Note that one should first create the appropriate [configs](../general/config.md).
 
 To get the help menu:
 ~~~

docs/pipelines/basty.md

@@ -30,7 +30,7 @@ java -jar Biopet.0.2.0.jar pipeline basty -h
 ~~~
 
 #### Run the pipeline:
-Note that one should first create the appropriate [configs](../config.md).
+Note that one should first create the appropriate [configs](../general/config.md).
 
 ~~~
 java -jar Biopet.0.2.0.jar pipeline basty -run -config MySamples.json -config MySettings.json -outDir myOutDir

docs/pipelines/flexiprep.md

-# Introduction
+# Flexiprep
+
+## Introduction
+Flexiprep is out quality control pipeline. This pipeline checks for possible barcode contamination, clips reads, trims reads and runs
+the tool <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" target="_blank">Fastqc</a>.
+The adapter clipping is performed by <a href="https://github.com/marcelm/cutadapt" target="_blank">Cutadapt</a>.
+For the quality trimming we use: <a href="https://github.com/najoshi/sickle" target="_blank">Sickle</a>. Flexiprep works on `.fastq` files.
+
+
+## Example
+
+To get the help menu:
+~~~
+java -jar Biopet-0.2.0-DEV.jar pipeline Flexiprep -h
+Arguments for Flexiprep:
+ -R1,--input_r1 <input_r1>                       R1 fastq file (gzipped allowed)
+ -sample,--samplename <samplename>               Sample name
+ -library,--libraryname <libraryname>            Library name
+ -outDir,--output_directory <output_directory>   Output directory
+ -R2,--input_r2 <input_r2>                       R2 fastq file (gzipped allowed)
+ -skiptrim,--skiptrim                            Skip Trim fastq files
+ -skipclip,--skipclip                            Skip Clip fastq files
+ -config,--config_file <config_file>             JSON config file(s)
+ -DSC,--disablescatterdefault                    Disable all scatters
+~~~
+
+As we can see in the above example we provide the options to skip trimming or clipping 
+since sometimes you want to have the possibility to not perform these tasks e.g.
+if there are no adapters present in your .fastq. Note that the pipeline also works on unpaired reads where one should only provide R1.
+
+
+To start the pipeline (remove `-run` for a dry run):
+~~~bash
+java -jar Biopet-0.2.0.jar pipeline Flexiprep -run -outDir myDir \
+-R1 myFirstReadPair -R2 mySecondReadPair -sample mySampleName \
+-library myLibname -config mySettings.json
+~~~
 
-# [Flexiprep](https://git.lumc.nl/biopet/biopet/tree/develop/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep)
-
-QC pipeline for fastq files
-
-### Commandline options
-
-
-| Argument | Explain |
-| -------- | ------- |
-| -R1,--input_r1 <input_r1> | R1 fastq file (gzipped allowed) |
-| -outputDir,--outputdir <outputdir> | Output directory |
-| -config,--configfiles <configfiles> | Config Json file |
-| -R2,--input_r2 <input_r2> | R2 fastq file (gzipped allowed) |
-| -skiptrim,--skiptrim | Skip Trim fastq files |
-| -skipclip,--skipclip | Skip Clip fastq files |
-
----
-
-### Config options
-
-
-| Config Name | Name |  Type | Default | Function |
-| ----------- | ---- | ----- | ------- | -------- |
-| flexiprep | skip_native_link |  Boolean | false | Do not make a link to the final file with name: <sample>.qc.<fastq extension> |
-| flexiprep | skiptrim | Boolean | false |  |
-| flexiprep | skiptrim | Boolean | false |  |
-
----
-
-### sub Module options
-
-
-This can be used in the root of the config or within the flexiprep, within flexiprep got prio over the root value
-
-| Config Name | Name | Type | Default | Function |
-| ----------- | ---- | ---- | ------- | -------- |
-| cutadapt | exe |  String | cutadapt | Excuteble for cutadapt |
-| cutadapt | default_clip_mode |  String | 3 | Do not make a link with name: <sample>.qc.<fastq extension> |
-| cutadapt | adapter |  Array[String] |  |  |
-| cutadapt | anywhere |  Array[String] |  |  |
-| cutadapt | front |  Array[String] |  |  |
-| cutadapt | discard |  Boolean | false |  |
-| cutadapt | opt_minimum_length |  Int | 1 |  |
-| cutadapt | opt_maximum_length | Int |  |  |
-| fastqc | exe | String | fastqc | Excuteble for fastqc |
-| fastqc->java | kmers |  String | java | Excuteble for java for fastqc |
-| fastqc | kmers | Int | 5 |  |
-| fastqc | quiet | Boolean | false |  |
-| fastqc | noextract | Boolean | false |  |
-| fastqc | nogroup | Boolean | false |  |
-| sickle | exe | String | sickle | Excuteble for sickle |
-| sickle | qualitytype | String |  |  |
-| sickle | defaultqualitytype | String | sanger | use this when quality type can't be found at fastqc |
-
----
-
-### License
-
-A dual licensing model is applied. The source code within this project is freely available for non-commercial use under an AGPL license; For commercial users or users who do not want to follow the AGPL license, please contact sasc@lumc.nl to purchase a separate license.
-
-# Example
-Note that one should first create the appropriate [configs](../config.md).
-
-# Testcase A
-
-# Testcase B
+## Result files
+The results from this pipeline will be a fastq file which is depending on the options either clipped and trimmed, only clipped,
+ only trimmed or no quality control at all. The pipeline also outputs 2 Fastqc runs one before and one after quality control.
+
+### Example output
+
+~~~
+.
+├── mySample_01.qc.summary.json
+├── mySample_01.qc.summary.json.out
+├── mySample_01.R1.contams.txt
+├── mySample_01.R1.fastqc
+│   ├── mySample_01.R1_fastqc
+│   │   ├── fastqc_data.txt
+│   │   ├── fastqc_report.html
+│   │   ├── Icons
+│   │   │   ├── error.png
+│   │   │   ├── fastqc_icon.png
+│   │   │   ├── tick.png
+│   │   │   └── warning.png
+│   │   ├── Images
+│   │   │   └── warning.png
+│   │   ├── Images
+│   │   │   ├── duplication_levels.png
+│   │   │   ├── kmer_profiles.png
+│   │   │   ├── per_base_gc_content.png
+│   │   │   ├── per_base_n_content.png
+│   │   │   ├── per_base_quality.png
+│   │   │   ├── per_base_sequence_content.png
+│   │   │   ├── per_sequence_gc_content.png
+│   │   │   ├── per_sequence_quality.png
+│   │   │   └── sequence_length_distribution.png
+│   │   └── summary.txt
+│   └── mySample_01.R1.qc_fastqc.zip
+├── mySample_01.R1.qc.fastq.gz
+├── mySample_01.R1.qc.fastq.gz.md5
+├── mySample_01.R2.contams.txt
+├── mySample_01.R2.fastqc
+│   ├── mySample_01.R2_fastqc
+│   │   ├── fastqc_data.txt
+│   │   ├── fastqc_report.html
+│   │   ├── Icons
+│   │   │   ├── error.png
+│   │   │   ├── fastqc_icon.png
+│   │   │   ├── tick.png
+│   │   │   └── warning.png
+│   │   ├── Images
+│   │   │   ├── duplication_levels.png
+│   │   │   ├── kmer_profiles.png
+│   │   │   ├── per_base_gc_content.png
+│   │   │   ├── per_base_n_content.png
+│   │   │   ├── per_base_quality.png
+│   │   │   ├── per_base_sequence_content.png
+│   │   │   ├── per_sequence_gc_content.png
+│   │   │   ├── per_sequence_quality.png
+│   │   │   └── sequence_length_distribution.png
+│   │   └── summary.txt
+│   └── mySample_01.R2_fastqc.zip
+├── mySample_01.R2.fastq.md5
+├── mySample_01.R2.qc.fastqc
+│   ├── mySample_01.R2.qc_fastqc
+│   │   ├── fastqc_data.txt
+│   │   ├── fastqc_report.html
+│   │   ├── Icons
+│   │   │   ├── error.png
+│   │   │   ├── fastqc_icon.png
+│   │   │   ├── tick.png
+│   │   │   └── warning.png
+│   │   ├── Images
+│   │   │   ├── duplication_levels.png
+│   │   │   ├── kmer_profiles.png
+│   │   │   ├── per_base_gc_content.png
+│   │   │   ├── per_base_n_content.png
+│   │   │   ├── per_base_quality.png
+│   │   │   ├── per_base_sequence_content.png
+│   │   │   ├── per_sequence_gc_content.png
+│   │   │   ├── per_sequence_quality.png
+│   │   │   └── sequence_length_distribution.png
+│   │   └── summary.txt
+│   └── mySample_01.R2.qc_fastqc.zip
+├── mySample_01.R2.qc.fastq.gz
+└── mySample_01.R2.qc.fastq.gz.md5
+~~~
 
-# Examine results
 
-## Result files
 
 ## Best practice
 

docs/pipelines/gentrap.md

@@ -3,7 +3,7 @@
 # Invocation
 
 # Example
-Note that one should first create the appropriate [configs](../config.md).
+Note that one should first create the appropriate [configs](../general/config.md).
 
 # Testcase A
 

docs/pipelines/mapping.md

@@ -19,7 +19,7 @@ After the QC, the pipeline simply maps the reads with the chosen aligner. The re
 ----
 
 ## Example
-Note that one should first create the appropriate [configs](../config.md).
+Note that one should first create the appropriate [configs](../general/config.md).
 
 For the help menu:
 ~~~
@@ -52,9 +52,11 @@ Arguments for Mapping:
 
 To run the pipeline:
 ~~~
-java -jar Biopet.0.2.0.jar pipeline mapping -run --config mySamples.json --config mySettings.json
+java -jar Biopet.0.2.0.jar pipeline mapping -run --config mySettings.json \
+-R1 myReads1.fastq -R2 myReads2.fastq -outDir myOutDir -OutputName myReadsOutput \
+-R hg19.fasta -RGSM mySampleName -RGLB myLib1
 ~~~
-__Note that the pipeline also accepts sample specification through command line but we encourage you to use the sample config__
+Note that removing -R2 causes the pipeline to be able of handlind single end `.fastq` files.
 
 To perform a dry run simply remove `-run` from the commandline call.
 

docs/pipelines/sage.md

@@ -6,13 +6,15 @@ The Sage pipeline has been created to process SAGE data, which requires a differ
 
 * [Flexiprep](flexiprep.md)
 * [Mapping](mapping.md)
-* [SageCountFastq](sagetools.md)
-* [SageCreateLibrary](sagetools.md)
-* [SageCreateTagCounts](sagetools.md)
+* [SageCountFastq](../tools/sagetools.md)
+* [SageCreateLibrary](../tools/sagetools.md)
+* [SageCreateTagCounts](../tools/sagetools.md)
 
 
 # Example
-Note that one should first create the appropriate [configs](../config.md).
+Note that one should first create the appropriate [configs](../general/config.md).
+
+To get the help menu:
 ~~~
 java -jar Biopet-0.2.0.jar pipeline Sage -h
 Arguments for Sage:
@@ -25,6 +27,11 @@ Arguments for Sage:
  -DSC,--disablescatterdefault                    Disable all scatters
 ~~~
 
+To run the pipeline:
+~~~
+ java -jar Biopet-0.2.0-DEV-801b72ed.jar pipeline Sage -run --config MySamples.json --config --MySettings.json
+~~~
+
 
 # Examine results
 

docs/pipelines/yamsvp.md

@@ -3,7 +3,7 @@
 # Invocation
 
 # Example
-Note that one should first create the appropriate [configs](../config.md).
+Note that one should first create the appropriate [configs](../general/config.md).
 
 # Testcase A
 

docs/tools/BiopetFlagstat.md

+# BiopetFlagstat
+
+## Introduction
+This tool has been created to extract all the metrics from a required bam file.
+It captures for example the # of mapped reads, # of duplicates, # of mates unmapped, # of reads with a certain mapping quality etc. etc.
+
+
+## Example
+To get the help menu:
+~~~
+java -jar Biopet-0.2.0.jar tool BiopetFlagstat -h
+Usage: BiopetFlagstat [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <file> | --inputFile <file>
+        out is a required file property
+  -r <chr:start-stop> | --region <chr:start-stop>
+        out is a required file property
+~~~
+
+To run the tool:
+~~~
+java -jar Biopet-0.2.0.jar tool BiopetFlagstat -I myBAM.bam
+~~~
+
+### Output
+
+|Number	|Total Flags|	Fraction|	Name|
+|------ | --------  | --------- | ------|
+|1	|862623034|	100.0000%|	All|
+|2	|861096240|	99.8230%|	Mapped|
+|3	|26506366|	3.0728%|	Duplicates|
+|4	|431233321|	49.9909%|	FirstOfPair|
+|5	|431389713|	50.0091%|	SecondOfPair|
+|6	|430909871|	49.9534%|	ReadNegativeStrand|
+|7	|0|	0.0000%|	NotPrimaryAlignment|
+|8	|862623034|	100.0000%|	ReadPaired|
+|9	|803603283|	93.1581%|	ProperPair|
+|10	|430922821|	49.9549%|	MateNegativeStrand|
+|11	|1584255|	0.1837%|	MateUnmapped|
+|12	|0|	0.0000%|	ReadFailsVendorQualityCheck|
+|13	|1380318|	0.1600%|	SupplementaryAlignment|
+|14	|1380318|	0.1600%|	SecondaryOrSupplementary|
+|15	|821996241|	95.2903%|	MAPQ>0|
+|16	|810652212|	93.9753%|	MAPQ>10|
+|17	|802852105|	93.0710%|	MAPQ>20|
+|18	|789252132|	91.4944%|	MAPQ>30|
+|19	|770426224|	89.3120%|	MAPQ>40|
+|20	|758373888|	87.9149%|	MAPQ>50|
+|21	|0|	0.0000%|	MAPQ>60|
+|22	|835092541|	96.8085%|	First normal, second read inverted (paired end orientation)|
+|23	|765156|	0.0887%|	First normal, second read normal|
+|24	|624090|	0.0723%|	First inverted, second read inverted|
+|25	|11537740|	1.3375%|	First inverted, second read normal|
+|26	|1462857|	0.1696%|	Mate in same strand|
+|27	|11751691|	1.3623%|	Mate on other chr|
\ No newline at end of file

docs/tools/CheckAllelesVcfInBam.md

+# CheckAllelesVcfInBam
+
+## Introduction
+This tool has been written to check the allele frequency in BAM files.
+
+## Example
+To get the help menu:
+~~~
+java -jar Biopet-0.2.0.jar tool CheckAllelesVcfInBam -h
+Usage: CheckAllelesVcfInBam [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <file> | --inputFile <file>
+        
+  -o <file> | --outputFile <file>
+        
+  -s <value> | --sample <value>
+        
+  -b <value> | --bam <value>
+        
+  -m <value> | --min_mapping_quality <value>
+~~~
+
+To run the tool:
+~~~
+java -jar Biopet-0.2.0.jar tool CheckAllelesVcfInBam --inputFile myVCF.vcf \
+--bam myBam1.bam --sample bam_sample1 --outputFile myAlleles.vcf
+
+~~~
+Note that the tool can run multiple BAM files at once.
+The only thing one needs to make sure off is matching the `--bam` and `--sample` in that same order.
+
+For multiple bam files:
+~~~
+java -jar Biopet-0.2.0.jar tool CheckAllelesVcfInBam --inputFile myVCF.vcf \
+--bam myBam1.bam --sample bam_sample1 --bam myBam2.bam --sample bam_sample2 \
+--bam myBam3.bam --sample bam_sample3 --outputFile myAlleles.vcf
+~~~
+
+## Output
+outputFile = VCF file which contains an extra field with the allele frequencies per sample given to the tool.

docs/tools/ExtractAlignedFastq.md

+# ExtractAlignedFastq
+
+## Introduction
+This tool extracts reads from a BAM file based on alignment intervals.
+E.g if one is interested in a specific location this tool extracts the full reads from the location.
+The tool is also very usefull to create test data sets.
+
+
+## Example
+To get the help menu:
+~~~
+java -jar Biopet-0.2.0.jar tool ExtractAlignedFastq -h
+ExtractAlignedFastq - Select aligned FASTQ records
+      
+Usage: ExtractAlignedFastq [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <bam> | --input_file <bam>
+        Input BAM file
+  -r <interval> | --interval <interval>
+        Interval strings
+  -i <fastq> | --in1 <fastq>
+        Input FASTQ file 1
+  -j <fastq> | --in2 <fastq>
+        Input FASTQ file 2 (default: none)
+  -o <fastq> | --out1 <fastq>
+        Output FASTQ file 1
+  -p <fastq> | --out2 <fastq>
+        Output FASTQ file 2 (default: none)
+  -Q <value> | --min_mapq <value>
+        Minimum MAPQ of reads in target region to remove (default: 0)
+  -s <value> | --read_suffix_length <value>
+        Length of common suffix from each read pair (default: 0)
+
+This tool creates FASTQ file(s) containing reads mapped to the given alignment intervals.
+~~~
+
+To run the tool:
+~~~
+java -jar Biopet-0.2.0.jar tool ExtractAlignedFastq \
+--input_file myBam.bam --in1 myFastq_R1.fastq --out1 myOutFastq_R1.fastq --interval myTarget.bed
+~~~
+* Note that this tool works for single end and paired end data. The above example can be easily extended for paired end data.
+The only thing one should add is: `--in2 myFastq_R2.fastq --out2 myOutFastq_R2.fastq`
+* The interval is just a genomic position or multiple genomic positions wherefrom one wants to extract the reads.
+
+
+## Output
+The output of this tool will be fastq files containing only mapped reads with the given alignment intervals extracted from the bam file.
\ No newline at end of file

docs/tools/FastqSplitter.md

+# FastqSplitter
+
+## Introduction
+This tool splits a fastq files based on the number of output files specified. So if one specifies 5 output files it will split the fastq
+into 5 files. This can be very usefull if one wants to use chunking option in one of our pipelines, we can generate the exact amount of fastqs
+needed for the number of chunks specified. Note that this will be automatically done inside the pipelines.  
+
+
+## Example
+To get the help menu:
+~~~
+java -jar Biopet-0.2.0.jar tool FastqSplitter -h
+Usage: FastqSplitter [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <file> | --inputFile <file>
+        out is a required file property
+  -o <file> | --output <file>
+        out is a required file property
+~~~
+To run the tool:
+~~~
+java -jar Biopet-0.2.0.jar tool FastqSplitter --inputFile myFastq.fastq \
+--output mySplittedFastq_1.fastq --output mySplittedFastq_2.fastq \