| Previous changeset 0:e41ec5af7472 (2018-08-02) Next changeset 2:704c401e0afb (2020-01-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed |
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modified:
heinz.xml heinz_scoring.py |
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| diff -r e41ec5af7472 -r 5f589c91566e heinz.xml --- a/heinz.xml Thu Aug 02 11:57:44 2018 -0400 +++ b/heinz.xml Tue Oct 30 18:57:02 2018 -0400 |
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| @@ -4,13 +4,13 @@ <requirement type="package" version="2.0">heinz</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ -heinz -m \${GALAXY_SLOTS:-2} -n '$score' -e '$edge' 1> '$subnetwork' +heinz -m \${GALAXY_SLOTS:-2} -n '$score' -e '$edge' > '$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" /> + <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" /> @@ -43,16 +43,15 @@ the second, Heinz score. ========= =================== -BRCA2 -6.991782933819368 +BRCA2 -6.991782933819368 --------- ------------------- -BRCA1 -5.206139799106934 +BRCA1 -5.206139799106934 --------- ------------------- -AACS -0.9299868303078357 +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 @@ -67,8 +66,6 @@ --------- --------- NPTX1 CIAO1 ========= ========= - - ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btn161</citation> |
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| diff -r e41ec5af7472 -r 5f589c91566e heinz_scoring.py --- a/heinz_scoring.py Thu Aug 02 11:57:44 2018 -0400 +++ b/heinz_scoring.py Tue Oct 30 18:57:02 2018 -0400 |
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| @@ -85,10 +85,7 @@ # Calculate the scores input_pvalues = pd.read_csv(args.nodes, sep='\t', names=['node', 'pvalue']) input_pvalues.loc[:, 'score'] = input_pvalues.pvalue.apply(lambda x: - (alpha - 1) * - (np.log(x) - - np.log( - p_threshold))) + (alpha - 1) * (np.log(x) - np.log(p_threshold))) # print(input_pvalues.loc[:, ['node', 'score']]) input_pvalues.loc[:, ['node', 'score']].to_csv(args.output, sep='\t', index=False, header=False) |