annotate picard_AddCommentsToBam.xml @ 33:3f254c5ced1d draft default tip

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

<tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>add comments to BAM dataset</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@
    ## linking does not work, picard complains about not writable file. Hopefully this can be removed in future version.
    ##@symlink_element_identifier@
    #import re
    #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
    cp '$inputFile' '$escaped_element_identifier' &&

    picard
      AddCommentsToBam
      --INPUT '$escaped_element_identifier'
      --OUTPUT '${outFile}'
      #for $element in $comments:
          --COMMENT '${element.comment}'
      #end for
      --QUIET true
      --VERBOSITY ERROR
      --VALIDATION_STRINGENCY ${validation_stringency}
  ]]></command>
    <inputs>
        <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
        <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
            <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
        </repeat>
        <expand macro="VS"/>
    </inputs>
    <outputs>
        <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
    </outputs>
    <tests>
        <test>
            <param name="inputFile" value="picard_AddCommentsToBam.bam"/>
            <param name="comment" value="test1"/>
            <param name="validation_stringency" value="LENIENT"/>
            <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

Adds one or more comments (@CO) to the header of a specified BAM dataset.

@dataset_collections@

@description@

  COMMENT=String
  C=String          Comments to add to the BAM file  This option may be specified 0 or more times.

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