view picard_SamFormatConverter.xml @ 26:30ee72a4ca0c draft

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<tool name="Picard SAM Format Converter" id="picard_SFC" version="0.1.0">
  <requirements><requirement type="package">picard</requirement></requirements>
  <command interpreter="python">
    picard_wrapper.py
      --input="$inputFile"
      --output-format=$outputFormat
      --output=$outFile
      -j "\$JAVA_JAR_PATH/SamFormatConverter.jar"
  </command>
  <inputs>
    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM"
      help="If empty, upload or import a SAM/BAM dataset." />
    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output bam instead of sam" help="Uncheck for sam output"/>
  </inputs>
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat} with read groups replaced">
      <change_format>
        <when input="outputFormat" value="sam" format="sam" />
      </change_format>
    </data>
  </outputs>
  <tests>
    <test>
      <!-- Command for replacing read groups in bam:
java -jar SamFormatConverter.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_SFC_input1.sam O=picard_SFC_output1.sam·
-->
      <param name="inputFile" value="picard_ARRG_input1.bam" />
      <param name="outputFormat" value="False" />
      <output name="outFile" file="picard_ARRG_output1.sam" ftype="sam" />
    </test>
    <test>
      <!-- Command for replacing read groups in sam:
java -jar AddOrReplaceReadGroups.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_ARRG_input1.sam O=picard_ARRG_output2.sam RGLB=LIB RGPL=IL RGPU=PL
picard_ARRG_input1.bam can be created from picard_ARRG_input1.sam
-->
      <param name="inputFile" value="picard_ARRG_input1.sam" />
      <output name="outFile" file="picard_ARRG_output2.sam" ftype="sam" />
    </test>
  </tests>
  <help>

.. class:: infomark

**Purpose**

Convert a BAM file to a SAM file, or BAM to SAM.

This is a Galaxy wrapper for SamFormatConverter, a part of the external package Picard-tools_.

 .. _Picard-tools: http://www.google.com/search?q=picard+samtools

------

.. class:: infomark

**Inputs, outputs, and parameters**

Either a sam file or a bam file must be supplied. If a bam file is used, it must
be coordinate-sorted. Galaxy currently coordinate-sorts all bam files.

The output file is either bam (the default) or sam, according to user selection,
and contains the same information as the input file except for the appropraite
additional (or modified) read group tags. Bam is recommended since it is smaller.

**Warning on SAM/BAM quality**

Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
to be the only way to deal with SAM/BAM that cannot be parsed.


  </help>
</tool>