added start up sage docs

docs/pipelines/GATK-pipeline.md

@@ -4,7 +4,7 @@
 
 The GATK-pipeline is build for variant calling on NGS data (preferably Illumina data).
 It is based on the <a href="https://www.broadinstitute.org/gatk/guide/best-practices" target="_blank">best practices</a>) of GATK in terms of there approach to variant calling.
-The pipeline accepts ```.fastq & .bam``` files as <samplename>.
+The pipeline accepts ```.fastq & .bam``` files as input.
 
 ----
 

docs/pipelines/sage.md

 # Introduction
-The Sage pipeline has been created to process SAGE data, which requires a different approach than NGS data.
+The Sage pipeline has been created to process SAGE data, which requires a different approach than standard NGS data.
 
 
+# Tools for this pipeline
+
+* [Flexiprep](flexiprep.md)
+* [Mapping](mapping.md)
+* [SageCountFastq](sagetools.md)
+* [SageCreateLibrary](sagetools.md)
+* [SageCreateTagCounts](sagetools.md)
 
-# Invocation
 
 # Example
 Note that one should first create the appropriate [configs](../config.md).
 ~~~
-java -jar Biopet-0.2.0-DEV-801b72ed.jar pipeline Sage -h
+java -jar Biopet-0.2.0.jar pipeline Sage -h
 Arguments for Sage:
  -outDir,--output_directory <output_directory>   Output directory
  --countbed <countbed>                           countBed
@@ -20,13 +26,70 @@ Arguments for Sage:
 ~~~
 
 
-# Testcase A
-
-# Testcase B
-
 # Examine results
 
 ## Result files
+~~~
+.
+├── 1A
+│   ├── 1A-2.merge.bai
+│   ├── 1A-2.merge.bam
+│   ├── 1A.fastq
+│   ├── 1A.genome.antisense.counts
+│   ├── 1A.genome.antisense.coverage
+│   ├── 1A.genome.counts
+│   ├── 1A.genome.coverage
+│   ├── 1A.genome.sense.counts
+│   ├── 1A.genome.sense.coverage
+│   ├── 1A.raw.counts
+│   ├── 1A.tagcount.all.antisense.counts
+│   ├── 1A.tagcount.all.sense.counts
+│   ├── 1A.tagcount.antisense.counts
+│   ├── 1A.tagcount.sense.counts
+│   ├── run_1
+│   │   ├── 1A-1.bai
+│   │   ├── 1A-1.bam
+│   │   ├── flexiprep
+│   │   └── metrics
+│   └── run_2
+│       ├── 1A-2.bai
+│       ├── 1A-2.bam
+│       ├── flexiprep
+│       └── metrics
+├── 1B
+│   ├── 1B-2.merge.bai
+│   ├── 1B-2.merge.bam
+│   ├── 1B.fastq
+│   ├── 1B.genome.antisense.counts
+│   ├── 1B.genome.antisense.coverage
+│   ├── 1B.genome.counts
+│   ├── 1B.genome.coverage
+│   ├── 1B.genome.sense.counts
+│   ├── 1B.genome.sense.coverage
+│   ├── 1B.raw.counts
+│   ├── 1B.tagcount.all.antisense.counts
+│   ├── 1B.tagcount.all.sense.counts
+│   ├── 1B.tagcount.antisense.counts
+│   ├── 1B.tagcount.sense.counts
+│   ├── run_1
+│   │   ├── 1B-1.bai
+│   │   ├── 1B-1.bam
+│   │   ├── flexiprep
+│   │   └── metrics
+│   └── run_2
+│       ├── 1B-2.bai
+│       ├── 1B-2.bam
+│       ├── flexiprep
+│       └── metrics
+├── ensgene.squish.bed
+├── summary-33.tsv
+├── taglib
+    ├── no_antisense_genes.txt
+    ├── no_sense_genes.txt
+    └── tag.lib
+~~~
+
+
 
 ## Best practice
 

docs/tools/MpileupToVcf.md

@@ -11,13 +11,13 @@ so usually one does not want to safe these files.
 ## Example
 To start the tool:
 ~~~
-java -jar Biopet-0.2.0-DEV-801b72ed.jar tool mpileupToVcf
+java -jar Biopet-0.2.0.jar tool mpileupToVcf
 ~~~
 
 
 To open the help:
 ~~~bash
-java -jar Biopet-0.2.0-DEV-801b72ed.jar tool mpileupToVcf -h
+java -jar Biopet-0.2.0.jar tool mpileupToVcf -h
 Usage: MpileupToVcf [options]
 
   -l <value> | --log_level <value>

docs/tools/sagetools.md

+# SAGE tools
+
+
+## SageCountFastq
+~~~
+Usage: SageCountFastq [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <file> | --input <file>
+        
+  -o <file> | --output <file>
+~~~
+
+## SageCreateLibrary
+~~~
+Usage: SageCreateLibrary [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <file> | --input <file>
+        
+  -o <file> | --output <file>
+        
+  --tag <value>
+        
+  --length <value>
+        
+  --noTagsOutput <file>
+        
+  --noAntiTagsOutput <file>
+        
+  --allGenesOutput <file>
+
+~~~
+
+## SageCreateTagCounts
+~~~
+Usage: SageCreateTagCounts [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -I <file> | --input <file>
+        
+  -t <file> | --tagLib <file>
+        
+  --countSense <file>
+        
+  --countAllSense <file>
+        
+  --countAntiSense <file>
+        
+  --countAllAntiSense <file>
+~~~
\ No newline at end of file

mkdocs.yml

@@ -9,6 +9,8 @@ pages:
 - ['pipelines/sage.md', 'Pipelines', 'Sage']
 - ['tools/SamplesTsvToJson.md','tools','SamplesTsvToJson']
 - ['tools/BastyGenerateFasta.md','tools','BastyGenerateFasta']
+- ['tools/MpileupToVcf.md', 'tools', 'MpileupToVcf']
+- ['tools/sagetools.md', 'tools', 'Sagetools']
 - ['cluster/oge.md', 'OpenGridEngine']
 - ['about.md', 'About']
 - ['license.md', 'License']