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

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

<tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>sort SAM/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[
    #if $sort_order == "queryname":
        #set $output = "output.sam"
        ln -sf '${outFile}' output.sam &&
    #else:
        #set $output = $outFile
    #end if
    @java_options@
    @symlink_element_identifier@
    picard SortSam
    --INPUT '$escaped_element_identifier'
    --OUTPUT '${output}'
    --SORT_ORDER '${sort_order}'
    --QUIET true
    --VERBOSITY ERROR
    --VALIDATION_STRINGENCY ${validation_stringency}
  ]]></command>
    <inputs>
        <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
        <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate. Selecting Queryname will output SAM file, as Galaxy does not support BAM files that are not coordinate sorted.">
            <option value="coordinate" selected="True">Coordinate</option>
            <option value="queryname">Queryname</option>
        </param>
        <expand macro="VS"/>
    </inputs>
    <outputs>
        <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Alignment sorted in ${sort_order} order">
            <change_format>
                <when input="sort_order" value="queryname" format="sam"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <!-- This test fails when setting metadata on non-coordinate sorted bam files.
           This should be handled better in Galaxy (info as of release 16.0).
           Workaroudn is to produce queryname sorted sam files.
    <test>
      <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
      <param name="sort_order" value="queryname"/>
      <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/>
    </test>
  -->
        <test>
            <param name="inputFile" ftype="bam" value="picard_SortSam.bam"/>
            <param name="sort_order" value="queryname"/>
            <output name="outFile" file="picard_SortSam_test1.sam" ftype="sam" lines_diff="4" compare="contains"/>
        </test>
        <test>
            <param name="inputFile" ftype="bam" value="picard_SortSam.bam"/>
            <param name="sort_order" value="coordinate"/>
            <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

Sorts the input SAM or BAM.

@dataset_collections@

@description@

  SORT_ORDER=SortOrder
  SO=SortOrder          Sort order of output file. You can either sort by queryname or by coordinate.

 @more_info@

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