comparison rnachipintegrator_wrapper.xml @ 6:466c68008537 draft default tip

Updated for RnaChipIntegrator 3.0.0.

5:087d9872fb0d

  <macros>
    <import>rnachipintegrator_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="version_command" />
  <command interpreter="bash"><![CDATA[
  rnachipintegrator_wrapper.sh
  #if $peaks_in.metadata.chromCol
    --peak_cols=${peaks_in.metadata.chromCol},${peaks_in.metadata.startCol},${peaks_in.metadata.endCol}
  #end if
  #if str( $cutoff ) != ""
    --cutoff=$cutoff

      <output name="peaks_per_feature_summary" ftype="tabular"
	      file="peaks_per_feature6.summary" />
      <output name="features_per_peak_summary" ftype="tabular"
	      file="features_per_peak6.summary" />
    </test>
  </tests>
  <help>

.. class:: infomark

6:466c68008537

  <macros>
    <import>rnachipintegrator_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="version_command" />
  <command detect_errors="aggressive"><![CDATA[
  bash $__tool_directory__/rnachipintegrator_wrapper.sh
  #if $peaks_in.metadata.chromCol
    --peak_cols=${peaks_in.metadata.chromCol},${peaks_in.metadata.startCol},${peaks_in.metadata.endCol}
  #end if
  #if str( $cutoff ) != ""
    --cutoff=$cutoff

      <output name="peaks_per_feature_summary" ftype="tabular"
	      file="peaks_per_feature6.summary" />
      <output name="features_per_peak_summary" ftype="tabular"
	      file="features_per_peak6.summary" />
    </test>
    <!--
	RnaChipIntegrator +name=test +cutoff=130000 +edge=tes +xlsx features.txt peaks.txt
    -->
    <test>
      <param name="features_in" value="features.txt" ftype="tabular" />
      <param name="peaks_in" value="peaks.txt" ftype="tabular" />
      <param name="cutoff" value="130000" />
      <param name="edge" value="tes" />
      <output name="xlsx_out" file="peaks7.xlsx" compare="sim_size" />
      <output name="peaks_per_feature_out" ftype="tabular"
	      file="peaks_per_feature7.out" />
      <output name="features_per_peak_out" ftype="tabular"
	      file="features_per_peak7.out" />
    </test>
  </tests>
  <help>

.. class:: infomark