comparison picard_CleanSam.xml @ 8:e417b1d6288d draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e

7:08f69add4d06

    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    picard
    CleanSam
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    QUIET=true
    VERBOSITY=ERROR
    VALIDATION_STRINGENCY=${validation_stringency}
  ]]></command>
  
  <inputs>
    <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
    
    <expand macro="VS" />
    
  </inputs>
  
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
    </data>
  </outputs>
  
  
  <tests>
    <test>
      <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
      <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" />
    </test>
  </tests>
  
  <help>

.. class:: infomark

**Purpose**

Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are:

 1. to soft-clip an alignment that hangs off the end of its reference sequence.
 2. to set MAPQ to 0 if a read is unmapped.
 
@dataset_collections@
 
@more_info@

  </help>
</tool>

8:e417b1d6288d

    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@
    picard
    CleanSam
    INPUT='$inputFile.element_identifier'
    OUTPUT="${outFile}"
    QUIET=true
    VERBOSITY=ERROR
    VALIDATION_STRINGENCY=${validation_stringency}
  ]]></command>

  <inputs>
    <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>

    <expand macro="VS" />

  </inputs>

  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
    </data>
  </outputs>


  <tests>
    <test>
      <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
      <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" lines_diff="4"/>
    </test>
  </tests>

  <help>

.. class:: infomark

**Purpose**

Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are:

 1. to soft-clip an alignment that hangs off the end of its reference sequence.
 2. to set MAPQ to 0 if a read is unmapped.

@dataset_collections@

@more_info@

  </help>
</tool>