comparison picard_FixMateInformation.xml @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8

32:f9242e01365a

<tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">1</token>
  </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.

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

@more_info@

  </help>
  <expand macro="citations" />
</tool>

33:3f254c5ced1d

<tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description>
    <macros>
        <import>picard_macros.xml</import>
        <token name="@WRAPPER_VERSION@">0</token>
    </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.

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

@more_info@

  </help>
    <expand macro="citations"/>
</tool>