comparison picard_FixMateInformation.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
    FixMateInformation
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    ASSUME_SORTED=${assume_sorted}
    ADD_MATE_CIGAR=${add_mate_cigar}
    
    SORT_ORDER=coordinate
    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
  
  ]]></command>
  <inputs>
    <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
    <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
    <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>
 
    <expand macro="VS" />
    
  </inputs> 
  
  <outputs>
    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/>
  </outputs>
  
  <tests>
    <test>
      <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
      <param name="add_mate_cigar" value="True"/>
      <param name="assume_sorted" value="False"/>
      <param name="validation_stringency" value="LENIENT"/>
      <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/>
    </test>
  </tests>
  
  
  <help>

**Purpose**

Ensure that all mate-pair information is in sync between each read and it's mate pair. Reads marked with the secondary alignment flag are written to the output file unchanged.

@dataset_collections@

@description@

  ASSUME_SORTED=Boolean
  AS=Boolean                    If true, assume that the input file is queryname sorted, even if the header says 
                                otherwise.  Default value: false. 
  
  ADD_MATE_CIGAR=Boolean
  MC=Boolean                    Adds the mate CIGAR tag (MC) if true, does not if false.  Default value: true. 
  
@more_info@

  </help>
</tool>

8:e417b1d6288d

    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    picard
    FixMateInformation
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    ASSUME_SORTED=${assume_sorted}
    ADD_MATE_CIGAR=${add_mate_cigar}

    SORT_ORDER=coordinate
    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR

  ]]></command>
  <inputs>
    <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
    <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
    <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>

    <expand macro="VS" />

  </inputs>

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

  <tests>
    <test>
      <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
      <param name="add_mate_cigar" value="True"/>
      <param name="assume_sorted" value="False"/>
      <param name="validation_stringency" value="LENIENT"/>
      <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/>
    </test>
  </tests>


  <help>

**Purpose**

Ensure that all mate-pair information is in sync between each read and it's mate pair. Reads marked with the secondary alignment flag are written to the output file unchanged.

@dataset_collections@

@description@

  ASSUME_SORTED=Boolean
  AS=Boolean                    If true, assume that the input file is queryname sorted, even if the header says
                                otherwise.  Default value: false.

  ADD_MATE_CIGAR=Boolean
  MC=Boolean                    Adds the mate CIGAR tag (MC) if true, does not if false.  Default value: true.

@more_info@

  </help>
</tool>