annotate pathway_image.xml @ 14:8ae67e9fb6ff

Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]

<tool id="gd_pathway_image" name="Pathway Image" version="1.0.0">
  <description>: Draw a KEGG pathway, highlighting specified gene modules</description>

  <command interpreter="python">
    mkpthwpng.py
      "--input=${input}"
      "--output=${output}"
      "--KEGGpath=${pathway}"
      "--posKEGGclmn=${input.metadata.kegg_path}"
      "--KEGGgeneposcolmn=${input.metadata.kegg_gene}"
  </command>

  <inputs>
    <param name="input" type="data" format="gd_sap" label="Table">
      <validator type="metadata" check="kegg_gene,kegg_path" message="Missing KEGG gene code column and/or KEGG pathway code/name column metadata.  Click the pencil icon in the history item to edit/save the metadata attributes" />
    </param>
    <param name="pathway" type="select">
      <options from_file="gd.pathways.txt">
        <column name="value" index="1"/>
        <column name="name" index="2"/>
        <filter type="data_meta" ref="input" key="dbkey" column="0" separator="\t" />
      </options>
    </param>
  </inputs>

  <outputs>
    <data name="output" format="png" />
  </outputs>

  <tests>
    <test>
      <param name="input" value="test_in/sample.gd_sap" ftype="gd_sap" />
      <param name="pathway" value="cfa05214" />
      <output name="output" file="test_out/pathway_image/pathway_image.png" compare="sim_size" delta = "10000" />
    </test>
  </tests>

  <help>

**What it does**

This tool produces an image of an input KEGG pathway, highlighting the
modules representing genes in an input list.  NOTE:  a given gene can
be assigned to multiple modules, and different genes can be assigned to
the same module.

  </help>
</tool>