comparison je-markdupes.xml @ 5:e2d1b5e1eb11 draft

planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6

4:384b972e43bc

<tool id="je_markdupes" name="Je-MarkDuplicates" version="@VERSION_STRING@">
    <description>to filter BAM files for read duplicates taking UMIs into account</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>
    <version_command>echo '1.0'</version_command>
    <command interpreter="bash">
<![CDATA[
    je markdupes

    ## picard MarkDuplicates defaults
    INPUT="${inputFile}"

          <output name="outFile" file="markdupes_DNase_sorted_marked.bam" ftype="bam" lines_diff="2"/>
          <output name="metrics_file" file="markdupes_metrics.txt" ftype="txt" lines_diff="4"/>
        </test>
    </tests>


  <help>
<![CDATA[
**What it does**

Je MarkDupes: Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules taking into account
molecular barcodes (Unique Molecular Identifiers or UMIs) found in read header.

    Default value: 100. This option can be set to 'null'
    to clear the default value.

]]>
  </help>

</tool>

5:e2d1b5e1eb11

<tool id="je_markdupes" name="Je-MarkDuplicates" version="@VERSION_STRING@">
    <description>to filter BAM files for read duplicates taking UMIs into account</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>
    <expand macro="version_command" />
    <command>
<![CDATA[
    je markdupes

    ## picard MarkDuplicates defaults
    INPUT="${inputFile}"

          <output name="outFile" file="markdupes_DNase_sorted_marked.bam" ftype="bam" lines_diff="2"/>
          <output name="metrics_file" file="markdupes_metrics.txt" ftype="txt" lines_diff="4"/>
        </test>
    </tests>

    <help>
<![CDATA[
**What it does**

Je MarkDupes: Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules taking into account
molecular barcodes (Unique Molecular Identifiers or UMIs) found in read header.

    Default value: 100. This option can be set to 'null'
    to clear the default value.

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