Mercurial > repos > iuc > heinz
diff heinz.xml @ 0:e41ec5af7472 draft
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 |
parents | |
children | 5f589c91566e |
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--- /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>