proteore_clusterprofiler: cluster

annotate cluster_profiler.xml @ 7:4609346d8108 draft

planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba

author	proteore
date	Tue, 18 Dec 2018 09:21:32 -0500
parents	5e16cec55146
children	b29255864039

rev	line source
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	1 <tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.12.18">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	2 <description>(Human, Mouse, Rat)[clusterProfiler]</description>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	3 <requirements>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	4 <requirement type="package" version="3.4.1">R</requirement>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	6 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	7 <requirement type="package" version="3.5.0">bioconductor-org.Rn.eg.db</requirement>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	8 <requirement type="package" version="3.2.0">bioconductor-dose</requirement>
1 09ba28df72ad planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: 0 diff changeset	9 <requirement type="package" version="3.4.4">bioconductor-clusterprofiler</requirement>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	10 </requirements>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	11 <command detect_errors="exit_code"><![CDATA[
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	12 Rscript "$__tool_directory__/GO-enrich.R"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	13 #if $input.ids == "text"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	14 --input_type="text"
4 710414ebb6db planemo upload commit 0a42c3d46be24406936ca0036bb436e6e2524fd2-dirty proteore parents: 3 diff changeset	15 --input="$input.txt"
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	16 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	17 --input_type="file"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	18 --input="$input.file"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	19 --ncol="$input.ncol"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	20 --header="$input.header"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	21 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	22
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	23 --id_type="$idti.idtypein"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	24
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	25 --species="$species"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	26
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	27 #if $ggo.go_represent == "true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	28 --go_represent="true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	29 --level="$ggo.level"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	30 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	31 --go_represent="false"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	32 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	33
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	34 #if $ego.go_enrich == "true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	35 --go_enrich="true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	36 --pval_cutoff="$ego.pval"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	37 --qval_cutoff="$ego.qval"
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	38 #if $ego.universe.universe_option == "true"
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	39 #if $ego.universe.universe_input.universe_ids == "text"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	40 --universe_type="text"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	41 --universe="$ego.universe.universe_input.txt"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	42 #else
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	43 --universe_type="file"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	44 --universe="$ego.universe.universe_input.file"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	45 --uncol="$ego.universe.universe_input.ncol"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	46 --uheader="$ego.universe.universe_input.header"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	47 #end if
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	48 --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	49 #end if
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	50 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	51 --go_enrich="false"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	52 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	53
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	54 --plot="$ego.plot"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	55 --onto_opt="$ontology" > $log
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	56 ]]></command>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	57 <inputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	58 <conditional name="input" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	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)" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	60 <option value="text">Copy/paste your IDs</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	61 <option value="file" selected="true">Input file containing your IDs</option>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	62 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	63 <when value="text" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	64 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	65 <sanitizer>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	66 <valid initial="string.printable">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	67 <remove value="'"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	68 </valid>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	69 <mapping initial="none">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	70 <add source="'" target="__sq__"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	71 </mapping>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	72 </sanitizer>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	73 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	74 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	75 <when value="file" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	76 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	77 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	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' />
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	79 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	80 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	81 <conditional name="idti" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	82 <param name="idtypein" type="select" label="Select type/source of IDs" help="" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	83 <option value="Uniprot">UniProt accession number (e.g.:P31946)</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	84 <option value="Entrez">Entrez Gene ID (e.g.:4151)</option>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	85 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	86 <when value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	87 <when value="Entrez"/>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	88 </conditional>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	89 <param name="species" type="select" label="Species" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	90 <option value="org.Hs.eg.db">Human (Homo sapiens) </option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	91 <option value="org.Mm.eg.db">Mouse (Mus musculus) </option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	92 <option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	93 </param>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	94 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Select GO terms category" optional="false" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	95 <option value="CC">Cellular Component</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	96 <option value="BP">Biological Process</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	97 <option value="MF">Molecular Function</option>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	98 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	99 <conditional name="ggo">
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	100 <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Perform GO categories representation analysis?"/>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	101 <when value="true">
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	102 <param name="level" type="select" label="Ontology level (the higher this number, the deeper the GO level)">
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	103 <option value="1">1</option>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	104 <option value="2" selected="True">2</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	105 <option value="3">3</option>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	106 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	107 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	108 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	109 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	110 <conditional name="ego">
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	111 <param name="go_enrich" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Perform GO categories enrichment analysis?"/>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	112 <when value="true">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	113 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	114 <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	115 <conditional name="universe" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	116 <param name="universe_option" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Define your own background IDs?"/>
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	117 <when value="true">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	118 <conditional name="universe_input">
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	119 <param name="universe_ids" type="select" label="Enter your background IDs (UniProt Accession number or Entrez Gene ID)" help="Copy/paste or from a file (e.g. table)" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	120 <option value="text">Copy/paste your background IDs</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	121 <option value="file" selected="true">Input file containing your background IDs</option>
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	122 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	123 <when value="text" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	124 <param name="txt" type="text" label="Copy/paste your background IDs" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	125 <sanitizer>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	126 <valid initial="string.printable">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	127 <remove value="'"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	128 </valid>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	129 <mapping initial="none">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	130 <add source="'" target="__sq__"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	131 </mapping>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	132 </sanitizer>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	133 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	134 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	135 <when value="file" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	136 <param name="file" type="data" format="txt,tabular" label="Select file that contains your background IDs list" help="" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	137 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	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' />
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	139 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	140 </conditional>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	141 <conditional name="universe_idti" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	142 <param name="universe_idtypein" type="select" label="Select type of background IDs" help="" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	143 <option value="Uniprot">UniProt Accession number</option>
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	144 <option value="Entrez">Entrez Gene ID</option>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	145 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	146 <when value="Uniprot"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	147 <when value="Entrez"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	148 </conditional>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	149 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	150 <when value="false"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	151 </conditional>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	152 <param name="plot" type="select" display="checkboxes" multiple="true" label="Graphical display" optional="false">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	153 <option selected = "true" value="dotplot">dot-plot</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	154 <option value="barplot">bar-plot</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	155 </param>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	156 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	157 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	158 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	159 </inputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	160 <outputs>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	161 <data name="log" format="tsv" label="Cluster profiler" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	162 <collection type="list" label="clusterProfiler text files" name="text_output">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	163 <discover_datasets pattern="(?P<designation>.+\.tsv)" ext="tsv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	164 </collection>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	165 <collection type="list" label="clusterProfiler diagram outputs" name="graph_output" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	166 <discover_datasets pattern="(?P<designation>.+plot)" ext="png" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	167 </collection>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	168 </outputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	169 <tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	170 <test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	171 <conditional name="input">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	172 <param name="ids" value="file"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	173 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	174 <param name="header" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	175 <param name="ncol" value="c1"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	176 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	177 <conditional name="idti">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	178 <param name="idtypein" value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	179 </conditional>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	180 <param name="species" value="org.Hs.eg.db"/>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	181 <conditional name="ggo">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	182 <param name="go_represent" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	183 <param name="level" value="3"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	184 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	185 <conditional name="ego">
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	186 <param name="go_enrich" value="true"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	187 <conditional name="universe_input">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	188 <param name="universe_ids" value="file"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	189 <param name="file" value="background_ids.txt"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	190 <param name="header" value="true"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	191 <param name="ncol" value="c7"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	192 </conditional>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	193 <conditional name="universe_idti" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	194 <param name="universe_idtypein" value="Uniprot"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	195 </conditional>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	196 </conditional>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	197 <param name="ontology" value="CC,BP,MF"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	198 <param name="plot" value="dotplot,barplot"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	199 <output name="log" file="log.txt" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	200 <output_collection name="text_output">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	201 <element name="cluster_profiler_GGO_CC.csv" file="cluster_profiler_GGO_CC.csv" ftype="csv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	202 <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_GGO_BP.csv" ftype="csv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	203 <element name="cluster_profiler_GGO_MF.csv" file="cluster_profiler_GGO_MF.csv" ftype="csv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	204 <element name="cluster_profiler_EGO_CC.csv" file="cluster_profiler_EGO_CC.csv" ftype="csv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	205 <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_EGO_BP.csv" ftype="csv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	206 <element name="cluster_profiler_EGO_MF.csv" file="cluster_profiler_EGO_MF.csv" ftype="csv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	207 </output_collection>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	208 <output_collection name="graph_output">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	209 <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	210 <element name="GGO_BP_bar-plot" file="GGO_BP_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	211 <element name="GGO_MF_bar-plot" file="GGO_MF_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	212 <element name="EGO_CC_bar-plot" file="EGO_CC_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	213 <element name="EGO_BP_bar-plot" file="EGO_BP_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	214 <element name="EGO_CC_dot-plot" file="EGO_CC_dot-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	215 <element name="EGO_BP_dot-plot" file="EGO_BP_dot-plot" ftype="png"/>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	216 </output_collection>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	217 </test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	218 </tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	219 <help><![CDATA[
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	220
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	221 Description
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	222
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	223 This tool is based on R package clusterProfiler and allows to perform GO terms classification and enrichment analyses on gene/protein sets (e.g. given a set of genes that are up-regulated under certain conditions, an enrichment analysis will find which GO terms are over-represented (or under-represented) using annotations for that gene/protein set).
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	224
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	225 Given a list of IDs, this tool:
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	226
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	227 (i) performs gene classification based on GO distribution at a specific level,
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	228
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	229 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, compared to a background. User has the possibility to use background corresponding to the whole organism or to a user-defined list. In this latter case, we recommand to use the "Build tissue-specific expression dataset" ProteoRE tool to create this list according to your need.
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	230
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	231 -----
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	232
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	233 Input
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	234
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	235 Two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers) or by copy/pasting your IDs (separated by a space).
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	236
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	237 "Select type/source of IDs": only entrez gene ID (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946) are allowed. If your list is not in this form, please use the ID_Converter tool of ProteoRE.
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	238
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	239 -----
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	240
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	241 Parameters
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	242
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	243 "Species": the three supported species are Homo sapiens, Mus musculus and Rattus norvegicus
1 09ba28df72ad planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: 0 diff changeset	244
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	245 "Perform GO categories representation analysis?": classify genes based on their projection at a specific level of the GO corpus (see parameter below), and provides functions (set to "Yes")
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	246
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	247 "Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 3) (set to level "2" by default). In general the higher the level, the more semantically specific the term is.
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	248
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	249 "Perform GO categories enrichment analysis?": calculate enrichment test for GO terms based on hypergeometric distribution (set to "Yes")
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	250
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	251 "P-value cut off": P-value threshold value for the declaration of significance (default is < 0.01)
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	252
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	253 "Q-value cut off": to prevent high false discovery rate (FDR) in multiple testing, Q-values (adjusted P-values) are estimated for FDR control. (default is < 0.05)
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	254
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	255 "Define your own background IDs?": by default the whole genome/proteome is used as a reference background to compute the enrichment. As this reference set should normally only include genes/proteins that were monitored during your analysis, this option allows to provide your own background; this could be for instance, the total number of genes/proteins expressed in the tissue/sample under study.
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	256
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	257 If you want to use your own background, click on the "Yes" button. Your gene/protein set must be a list of Entrez gene ID or Uniprot accession number (otherwise, use the ID-Converter tool of ProteoRE). Select the file containing your list of ID (as background), then specify the column number which contains IDs and the type of IDs (gene Entrez or Uniprot Accession number) as requested.
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	258
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	259 Of note: for Human species, you can build your own background by using the "Build tissue-specific expression dataset" tool of ProteoRE.
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	260
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	261 -----
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	262
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	263 Output
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	264
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	265 Diagram output: graphical output in the form of bar-plot or dot-plot (png, jpeg or pdf format), one figure for each GO category.
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	266 Text tables: with the following information GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) and GO term frequency (e.g. BP.Frequency)d graphics representing the repartition and/or enrichment of GO categories. One table and one graphic will be produced for each GO catagory.
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	267
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	268 -----
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	269
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	270 Authors
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	271 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	272 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287. doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	273
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	274 User manual / Documentation of the clusterProfiler R package (functions and parameters):
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	275 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
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5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	277 -----
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	278
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	279 .. class:: infomark
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	280
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	281 Galaxy integration
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	282
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	283 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	284
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	285 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	286
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	287 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	288
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	289 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	290
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	291
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	292 ]]></help>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	293 <citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	294 </citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	295 </tool>

Mercurial > repos > proteore > proteore_clusterprofiler

annotate cluster_profiler.xml @ 7:4609346d8108 draft