comparison depth_of_coverage.xml @ 13:669a23f1f4b5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit e5a5ad091c621348dc6ce2df861475ebc54a380e

12:86007c982f00

<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.0">
  <description>on BAM files</description>
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="version_command" />
  <command interpreter="python">gatk2_wrapper.py
   ##--max_jvm_heap_fraction "1"
   --stdout "${output_log}"
   #for $i, $input_bam in enumerate( $reference_source.input_bams ):
       -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
       #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
           -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
       #end if
   #end for
   -p '
   @JAR_PATH@
    -T "DepthOfCoverage"
    \$GATK2_SITE_OPTIONS

  </command>
  <inputs>
    <conditional name="reference_source">
      <expand macro="reference_source_selector_param" />
      <when value="cached">
        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
            <param name="input_bam" type="data" format="bam" label="BAM file">
              <validator type="unspecified_build" />
              <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
            </param>
        </repeat>
        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
          <options from_data_table="gatk2_picard_indexes">
            <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
          </options>
          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
        </param>
      </when>
      <when value="history"> <!-- FIX ME!!!! -->
        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
            <param name="input_bam" type="data" format="bam" label="BAM file" />
        </repeat>
        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
      </when>
    </conditional>

    <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &amp;lt;calculateCoverageOverGenes&amp;gt;" />

13:669a23f1f4b5

<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.1">
  <description>on BAM files</description>
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="version_command" />
  <command interpreter="python">gatk2_wrapper.py
   ##--max_jvm_heap_fraction "1"
   --stdout "${output_log}"
   @BAM_INPUTS@
   -p '
   @JAR_PATH@
    -T "DepthOfCoverage"
    \$GATK2_SITE_OPTIONS

  </command>
  <inputs>
    <conditional name="reference_source">
      <expand macro="reference_source_selector_param" />
      <when value="cached">
        <expand macro="input_bams_cached" />
        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
          <options from_data_table="gatk2_picard_indexes">
            <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
          </options>
          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
        </param>
      </when>
      <when value="history"> <!-- FIX ME!!!! -->

        <expand macro="input_bams_history" />
        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
      </when>
    </conditional>

    <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &amp;lt;calculateCoverageOverGenes&amp;gt;" />