Merge branch 'fix-docs_tools' into 'develop'

Added text to args

Fixes #373 

See merge request !437

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala

@@ -34,28 +34,28 @@ object VcfToTsv extends ToolCommand {
   class OptParser extends AbstractOptParser {
     opt[File]('I', "inputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(inputFile = x)
-    }
+    } text "Input vcf file"
     opt[File]('o', "outputFile") maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(outputFile = x)
     } text "output file, default to stdout"
     opt[String]('f', "field") unbounded () action { (x, c) =>
       c.copy(fields = x :: c.fields)
-    }
+    } text "Genotype field to use" valueName "Genotype field name"
     opt[String]('i', "info_field") unbounded () action { (x, c) =>
       c.copy(infoFields = x :: c.infoFields)
-    }
+    } text "Info field to use" valueName "Info field name"
     opt[Unit]("all_info") unbounded () action { (x, c) =>
       c.copy(allInfo = true)
-    }
+    } text "Use all info fields in the vcf header"
     opt[Unit]("all_format") unbounded () action { (x, c) =>
       c.copy(allFormat = true)
-    }
+    } text "Use all genotype fields in the vcf header"
     opt[String]('s', "sample_field") unbounded () action { (x, c) =>
       c.copy(sampleFields = x :: c.sampleFields)
-    }
+    } text "Genotype fields to use in the tsv file"
     opt[Unit]('d', "disable_defaults") unbounded () action { (x, c) =>
       c.copy(disableDefaults = true)
-    }
+    } text "Don't output the default columns from the vcf file"
     opt[String]("separator") maxOccurs 1 action { (x, c) =>
       c.copy(separator = x)
     } text "Optional separator. Default is tab-delimited"

docs/tools/SamplesTsvToJson.md

@@ -27,7 +27,7 @@ Usage: SamplesTsvToJson [options]
 
 ~~~
 
-A user provides a TAB seperated file (TSV) with sample specific properties which are parsed into JSON format by the tool.
+A user provides a TAB separated file (TSV) with sample specific properties which are parsed into JSON format by the tool.
 For example, a user wants to add certain properties to the description of a sample, such as the treatment a sample received. Then a TSV file with an extra column called treatment is provided. 
 The resulting JSON file will have the 'treatment' property in it as well. The order of the columns is not relevant to the end result 
 

docs/tools/VcfToTsv.md

@@ -14,26 +14,33 @@ biopet tool VcfToTsv -h
 Usage: VcfToTsv [options]
 
   -l <value> | --log_level <value>
-        Log level
+        Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'
   -h | --help
         Print usage
   -v | --version
         Print version
   -I <file> | --inputFile <file>
-        
+        Input vcf file
   -o <file> | --outputFile <file>
         output file, default to stdout
-  -f <value> | --field <value>
-        
-  -i <value> | --info_field <value>
-        
+  -f Genotype field name | --field Genotype field name
+        Genotype field to use
+  -i Info field name | --info_field Info field name
+        Info field to use
   --all_info
-        
+        Use all info fields in the vcf header
   --all_format
-        
+        Use all genotype fields in the vcf header
   -s <value> | --sample_field <value>
-        
+        Genotype fields to use in the tsv file
   -d | --disable_defaults
+        Don't output the default columns from the vcf file
+  --separator <value>
+        Optional separator. Default is tab-delimited
+  --list_separator <value>
+        Optional list separator. By default, lists are separated by a comma
+  --max_decimals <value>
+        Number of decimal places for numbers. Default is 2
 ~~~
 
 To run the tool: