Edited wrappers for R scripts #81
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…clusterProfiler package)
…GG (using clusterProfiler package)
…GG (using clusterProfiler package)
…ow calls the r script directly (instead of calling r script from MultiPEN)
…ow calls the r script directly (instead of calling r script from MultiPEN)
…s, description of inputs and how to run Rscript
bgruening
reviewed
Apr 10, 2017
…al parameters for log2 transform, z-scores, decision threshold, max number of iterations
…al parameters for log2 transform, z-scores, decision threshold, max number of iterations; optional string is also added at the end of all output file name
nsoranzo
reviewed
May 5, 2017
nsoranzo
reviewed
May 5, 2017
nsoranzo
reviewed
May 5, 2017
| mv MultiPEN-Rankings_lambda${lambda}_${optionalParameters}.txt Rankings.txt && | ||
| mv MultiPEN-vts_lambda${lambda}_${optionalParameters}.txt vts.txt && | ||
| mv MultiPEN-Rankings_lambda${lambda}_genes-higher-in-cases_${optionalParameters}.txt Rankings-higherInCases.txt && | ||
| mv MultiPEN-Rankings_lambda${lambda}_genes-higher-in-control_${optionalParameters}.txt Rankings-higherInControl.txt |
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Add single quotes around all the MultiPEN-....txt filenames (again because ${optionalParameters} is a text param).
nsoranzo
requested changes
May 5, 2017
| <tool id="enrich kegg" name="enrich kegg" version="0.0.3"> | ||
| <description> over-representation and GSE analysis with KEGG</description> | ||
| <requirements> | ||
| <requirement type="package" version="3.3.1">r</requirement> |
| <requirements> | ||
| <requirement type="package" version="3.3.1">r</requirement> | ||
| <requirement type="package" version="3.0.5">bioconductor-clusterProfiler</requirement> | ||
| <requirement type="package" version="1.10">r-BBmisc</requirement> |
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As above, only version 1.9 is available in Bioconda, need to update the recipe there or decrease the version here.
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Renamed two wrappers (as they now call R scripts instead of MultiPEN standalone application):
Added one more wrapper: Rscript-STRINGdb-network.xml.
Added R scripts:
Edited MultiPEN-feature-selectiom.xml to include string with optional parameters for log2 transform, z-scores, decision threshold, max number of iterations.