annotate heinz.xml @ 0:e41ec5af7472 draft

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

<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>