Mercurial > repos > proteore > proteore_clusterprofiler

comparison cluster_profiler.xml @ 1:09ba28df72ad draft

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planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
author proteore
date Thu, 01 Mar 2018 10:41:32 -0500
parents bd052861852b
children a71792aa5a08
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0:bd052861852b 1:09ba28df72ad
2 <requirements> 2 <requirements>
3 <requirement type="package" version="3.4.1">R</requirement> 3 <requirement type="package" version="3.4.1">R</requirement>
4 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> 4 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
5 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement> 5 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
6 <requirement type="package" version="3.2.0">bioconductor-dose</requirement> 6 <requirement type="package" version="3.2.0">bioconductor-dose</requirement>
7 <requirement type="package" version="3.0.5">bioconductor-clusterprofiler</requirement> 7 <requirement type="package" version="3.4.4">bioconductor-clusterprofiler</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 Rscript "$__tool_directory__/GO-enrich.R" 10 Rscript "$__tool_directory__/GO-enrich.R"
11 #if $input.ids == "text" 11 #if $input.ids == "text"
12 --input_type="text" 12 --input_type="text"
165 (i) performs gene classification based on GO distribution at a specific level, or 165 (i) performs gene classification based on GO distribution at a specific level, or
166 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, 166 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list,
167 compared to a background (whole organism or user-defined list). 167 compared to a background (whole organism or user-defined list).
168 168
169 **Input required** 169 **Input required**
170 170
171 This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946). 171 This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946).
172 You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) where there are contained. 172 You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) where there are contained.
173 173
174 174
175 **Output** 175 **Output**