Mercurial > repos > proteore > proteore_clusterprofiler

comparison cluster_profiler.xml @ 9:2f67202ffdb3 draft

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planemo upload commit 6ca074d75447a272b570f7709ed10d0c8356bec5-dirty
author proteore
date Wed, 27 Feb 2019 03:39:16 -0500
parents b29255864039
children d951677a50d4
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8:b29255864039 9:2f67202ffdb3
1 <tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.12.21"> 1 <tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.02.18">
2 <description>(Human, Mouse, Rat)[clusterProfiler]</description> 2 <description>(Human, Mouse, Rat)[clusterProfiler]</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.4.1">R</requirement> 4 <requirement type="package" version="3.4.1">R</requirement>
5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> 5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
6 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement> 6 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
30 #else 30 #else
31 --go_represent="false" 31 --go_represent="false"
32 #end if 32 #end if
33 33
34 #if $ego.go_enrich == "true" 34 #if $ego.go_enrich == "true"
35 --plot="$ego.plot"
35 --go_enrich="true" 36 --go_enrich="true"
36 --pval_cutoff="$ego.pval" 37 --pval_cutoff="$ego.pval"
37 --qval_cutoff="$ego.qval" 38 --qval_cutoff="$ego.qval"
38 #if $ego.universe.universe_option == "true" 39 #if $ego.universe.universe_option == "true"
39 #if $ego.universe.universe_input.universe_ids == "text" 40 #if $ego.universe.universe_input.universe_ids == "text"
49 #end if 50 #end if
50 #else 51 #else
51 --go_enrich="false" 52 --go_enrich="false"
52 #end if 53 #end if
53 54
54 --plot="$ego.plot"
55 --onto_opt="$ontology" > $log 55 --onto_opt="$ontology" > $log
56 ]]></command> 56 ]]></command>
57 <inputs> 57 <inputs>
58 <conditional name="input" > 58 <conditional name="input" >
59 <param name="ids" type="select" label="Enter your IDs (UniProt Accession numer or Gene ID)" help="Copy/paste or from a file (e.g. table)" > 59 <param name="ids" type="select" label="Enter your IDs (UniProt Accession numer or Gene ID)" help="Copy/paste or from a file (e.g. table)" >
73 </param> 73 </param>
74 </when> 74 </when>
75 <when value="file" > 75 <when value="file" >
76 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" /> 76 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
77 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> 77 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
78 <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> 78 <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
79 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
80 </param>
79 </when> 81 </when>
80 </conditional> 82 </conditional>
81 <conditional name="idti" > 83 <conditional name="idti" >
82 <param name="idtypein" type="select" label="Select type/source of IDs" help="" > 84 <param name="idtypein" type="select" label="Select type/source of IDs" help="" >
83 <option value="Uniprot">UniProt accession number (e.g.:P31946)</option> 85 <option value="Uniprot">UniProt accession number (e.g.:P31946)</option>
133 </param> 135 </param>
134 </when> 136 </when>
135 <when value="file" > 137 <when value="file" >
136 <param name="file" type="data" format="txt,tabular" label="Select file that contains your background IDs list" help="" /> 138 <param name="file" type="data" format="txt,tabular" label="Select file that contains your background IDs list" help="" />
137 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> 139 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
138 <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> 140 <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
141 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
142 </param>
139 </when> 143 </when>
140 </conditional> 144 </conditional>
141 <conditional name="universe_idti" > 145 <conditional name="universe_idti" >
142 <param name="universe_idtypein" type="select" label="Select type of background IDs" help="" > 146 <param name="universe_idtypein" type="select" label="Select type of background IDs" help="" >
143 <option value="Uniprot">UniProt Accession number</option> 147 <option value="Uniprot">UniProt Accession number</option>