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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
author | iuc |
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date | Thu, 02 Aug 2018 11:57:44 -0400 |
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children | 5f589c91566e |
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<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>