comparison picard_MergeSamFiles.xml @ 0:2e42e3c01fcf draft

planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty

0:2e42e3c01fcf

<tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0">
  <description>merges multiple SAM/BAM datasets into one</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    #for $index, $listCollection in enumerate($inputList):
      && 
      picard
      MergeSamFiles

      #for $element in $listCollection:
        INPUT="${element}"
      #end for

      OUTPUT="${'merged{}.bam'.format($index)}"
      MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}"
      ASSUME_SORTED="${assume_sorted}"
      #for $element in $comments:
        COMMENT="${element.comment}"
      #end for
      USE_THREADING=true
      SORT_ORDER=coordinate
      VALIDATION_STRINGENCY="${validation_stringency}"
      QUIET=true
      VERBOSITY=ERROR 
    #end for
  ]]></command>
  <inputs>
    <param format="sam,bam" name="inputList" type="data_collection" collection_type="list:list" label="Select SAM/BAM dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
    <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/>
    <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>

    <repeat name="comments" title="Comment" min="0" 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 format="bam" name="merged">
        <discover_datasets pattern="__designation_and_ext__" visible="true" />
    </data>
  </outputs>

  <tests>
    <test>
      <param name="inputList">
        <collection type="list:list">
          <element name="list 1">
            <collection type="list">
              <element name="l1_input1" value="picard_MergeSamFiles_input1.bam" />
              <element name="l1_input2" value="picard_MergeSamFiles_input2.bam" />
              <element name="l1_input3" value="picard_MergeSamFiles_input3.bam" />
            </collection>
          </element>
          <element name="list 2">
            <collection type="list">
              <element name="l2_input1" value="picard_MergeSamFiles_input1.bam" />
              <element name="l2_input2" value="picard_MergeSamFiles_input2.bam" />
              <element name="l2_input3" value="picard_MergeSamFiles_input3.bam" />
            </collection>
          </element>
        </collection>
      </param>
      <param name="assume_sorted" value="False"/>
      <param name="merge_sequence_dictionaries" value="False"/>
      <param name="validation_stringency" value="LENIENT"/>
      <output name="merged0" ftype="bam">
        <assert_contents>
          <has_text text=""/>
        </assert_contents>
      </output>
      <output name="merged1" ftype="bam">
        <assert_contents>
          <has_text text=""/>
        </assert_contents>
      </output>
    </test>
  </tests>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <help>

**Purpose**

Merges multiple SAM/BAM datasets into one.

@dataset_collections@

@description@

  ASSUME_SORTED=Boolean
  AS=Boolean                    If true, assume that the input files are in the same sort order as the requested output
                                sort order, even if their headers say otherwise.  Default value: false. This option can
                                be set to 'null' to clear the default value. Possible values: {true, false}

  MERGE_SEQUENCE_DICTIONARIES=Boolean
  MSD=Boolean                   Merge the sequence dictionaries  Default value: false. This option can be set to 'null'
                                to clear the default value. Possible values: {true, false}

  COMMENT=String
  CO=String                     Comment(s) to include in the merged output file's header.  This option may be specified 0
                                or more times.


@more_info@

  </help>
</tool>