diff heinz.xml @ 0:e41ec5af7472 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/heinz.xml	Thu Aug 02 11:57:44 2018 -0400
@@ -0,0 +1,76 @@
+<tool id="heinz" name="Identify optimal scoring subnetwork" version="1.0">
+    <description>using Heinz</description>
+    <requirements>
+        <requirement type="package" version="2.0">heinz</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+heinz -m \${GALAXY_SLOTS:-2} -n '$score' -e '$edge' 1> '$subnetwork'
+    ]]></command>
+    <inputs>
+        <param type="data" name="score" format="txt" label="File containing Heinz scores"
+        help="The file should contain two columns: the node identifier (e.g. gene) and the corresponding Heinz score" />
+        <param type="data" name="edge" format="txt" label="Edge file"
+        help="In this file, two nodes define one edge, one edge per line" />
+    </inputs>
+    <outputs>
+        <data name="subnetwork" format="txt" label="${tool.name} on ${on_string}: Optimal subgraph" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="score" value="NodesPCST.txt" />
+            <param name="edge" value="EdgesPCST.txt" />
+            <output name="subnetwork">
+                <assert_contents>
+                    <has_text text='label="a\n5\n0\n0"' />
+                    <has_text text='label="b\n-4\n0\n1",shape=box' />
+                    <has_text text="Total weight: 36" />
+                    <has_text text="0 -- 1" />
+                    <has_text text="1 -- 3" />
+                    <has_text text="5 -- 7" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**Note**: You are currently using a version of Heinz based on IBM CPLEX Community version,
+which is limiting the capacity of Heinz in handling big networks. For an unlimited version of Heinz,
+you need to get a license of IBM CPLEX and compile Heinz from scratch from here https://github.com/ls-cwi/heinz.
+We are currently looking for an alternative to IBM CPLEX in Heinz to make an unlimited version of Heinz available
+to the public as soon as possible.
+
+Score file --- the output file of the tool "Calculate Heinz scores": two columns delimited
+by a tab without headers, the first column is node identifier (e.g., genes, KEGG ORTHOLOGY (KO));
+the second, Heinz score.
+
+========= ===================
+BRCA2    -6.991782933819368
+--------- -------------------
+BRCA1    -5.206139799106934
+--------- -------------------
+AACS     -0.9299868303078357
+--------- -------------------
+ABCC11    -5.845009850430119
+========= ===================
+
+
+Edge file: the background network Heinz uses in the form of a list of edges; each line is made up of
+two node identifiers (e.g., genes, KEGG ORTHOLOGY (KO)) delimited by a tab. In practice, we could
+prepare this file using different pathway databases, such as Reactome, STRING and KEGG. Which database
+to choose depends on the question to solve.
+
+========= =========
+ACTR1B    ACVR2B
+--------- ---------
+ZSWIM9    FOXP3
+--------- ---------
+LGALS4    PRKX
+--------- ---------
+NPTX1     CIAO1
+========= =========
+
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btn161</citation>
+    </citations>
+</tool>