comparison heinz.xml @ 1:5f589c91566e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed

0:e41ec5af7472

    <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>

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.

--------- ---------
LGALS4    PRKX
--------- ---------
NPTX1     CIAO1
========= =========


    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btn161</citation>
    </citations>
</tool>

1:5f589c91566e

    <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' > '$subnetwork'
    ]]></command>
    <inputs>
        <param name="score" type="data" format="txt" label="File containing Heinz scores"
            help="The file should contain two columns: the node identifier (e.g. gene) and the corresponding Heinz score" />
        <param name="edge" type="data" format="txt" label="Edge file"
            help="In this file, two nodes define one edge, one edge per line" />
    </inputs>
    <outputs>
        <data name="subnetwork" format="txt" label="${tool.name} on ${on_string}: Optimal subgraph" />
    </outputs>
    <tests>

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.

--------- ---------
LGALS4    PRKX
--------- ---------
NPTX1     CIAO1
========= =========
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btn161</citation>
    </citations>
</tool>