comparison rgPicardASMetrics.xml @ 2:93ace7e49295 draft

Uploaded valid tools.

1:ab5e8beab4fe

<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="1.56.0">
  <command interpreter="python">
    picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file"
    --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --datatype "$input_file.ext"
    -j \$JAVA_JAR_PATH/CollectAlignmentSummaryMetrics.jar  --tmpdir "${__new_file_path__}" 
#if $genomeSource.refGenomeSource == "history":
    --ref-file "$genomeSource.ownFile"
#else
    --ref "${genomeSource.index.fields.path}"
#end if
  </command>
  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>

        <option value="history">Use a genome (fasta format) from my history</option>
      </param>
      <when value="default">
        <param name="index" type="select" label="Check the assigned reference genome" help="Galaxy thinks that the reads in you dataset were aligned against this reference. If this is not correct, use the 'Select a build-in reference genome' option of the 'Select Reference Genome' dropdown to select approprtiate Reference.">
          <options from_data_table="all_fasta">
          <filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator="," />
          <validator type="no_options" message="No reference build available for selected input" /> 
          </options>
        </param>
      </when>
      <when value="indexed">

2:93ace7e49295

<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="1.56.0">
  <command interpreter="python">
    picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}"
    --assumesorted "${sorted}" -b "${bisulphite}" --adaptors "${adaptors}" --maxinsert "${maxinsert}" -n "${out_prefix}" --datatype "${input_file.ext}"
    -j \$JAVA_JAR_PATH/CollectAlignmentSummaryMetrics.jar  --tmpdir "${__new_file_path__}" 
#if $genomeSource.refGenomeSource == "history":
    --ref-file "${genomeSource.ownFile}"
#else
    --ref "${genomeSource.index.fields.path}"
#end if
  </command>
  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>

        <option value="history">Use a genome (fasta format) from my history</option>
      </param>
      <when value="default">
        <param name="index" type="select" label="Check the assigned reference genome" help="Galaxy thinks that the reads in you dataset were aligned against this reference. If this is not correct, use the 'Select a build-in reference genome' option of the 'Select Reference Genome' dropdown to select approprtiate Reference.">
          <options from_data_table="all_fasta">
          <filter type="data_meta" ref="input_file" key="dbkey" column="1" multiple="True" separator="," />
          <validator type="no_options" message="No reference build available for selected input" /> 
          </options>
        </param>
      </when>
      <when value="indexed">