diff pathway_image.xml @ 14:8ae67e9fb6ff

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pathway_image.xml	Fri Sep 28 11:35:56 2012 -0400
@@ -0,0 +1,48 @@
+<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>