proteore_clusterprofiler: cluster

annotate cluster_profiler.xml @ 10:d951677a50d4 draft

planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty

author	proteore
date	Fri, 28 Jun 2019 05:08:48 -0400
parents	2f67202ffdb3
children	cc2bd0d2afa2

rev	line source
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	1 <tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.06.27.1">
7 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 $ego.go_enrich == "true"
9 2f67202ffdb3 planemo upload commit 6ca074d75447a272b570f7709ed10d0c8356bec5-dirty proteore parents: 8 diff changeset	35 --plot="$ego.plot"
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	36 --go_enrich="true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	37 --pval_cutoff="$ego.pval"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	38 --qval_cutoff="$ego.qval"
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	39 #if $ego.universe.universe_option == "true"
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	40 #if $ego.universe.universe_input.universe_ids == "text"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	41 --universe_type="text"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	42 --universe="$ego.universe.universe_input.txt"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	43 #else
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	44 --universe_type="file"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	45 --universe="$ego.universe.universe_input.file"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	46 --uncol="$ego.universe.universe_input.ncol"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	47 --uheader="$ego.universe.universe_input.header"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	48 #end if
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	49 --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	50 #end if
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	51 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	52 --go_enrich="false"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	53 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	54
7 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" >
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	59 <param name="ids" type="select" label="Enter your IDs (UniProt Accession number or Gene ID)" help="Copy/paste or from a file (e.g. table)" >
7 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?" />
9 2f67202ffdb3 planemo upload commit 6ca074d75447a272b570f7709ed10d0c8356bec5-dirty proteore parents: 8 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'>
2f67202ffdb3 planemo upload commit 6ca074d75447a272b570f7709ed10d0c8356bec5-dirty proteore parents: 8 diff changeset	79 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
2f67202ffdb3 planemo upload commit 6ca074d75447a272b570f7709ed10d0c8356bec5-dirty proteore parents: 8 diff changeset	80 </param>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	81 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	82 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	83 <conditional name="idti" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	84 <param name="idtypein" type="select" label="Select type/source of IDs" help="" >
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	85 <option value="Uniprot">UniProt accession number (e.g. P31946)</option>
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	86 <option value="Entrez">Entrez Gene ID (e.g. 4151)</option>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	87 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	88 <when value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	89 <when value="Entrez"/>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	90 </conditional>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	91 <param name="species" type="select" label="Species" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	92 <option value="org.Hs.eg.db">Human (Homo sapiens) </option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	93 <option value="org.Mm.eg.db">Mouse (Mus musculus) </option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	94 <option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	95 </param>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	96 <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	97 <option value="CC">Cellular Component</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	98 <option value="BP">Biological Process</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	99 <option value="MF">Molecular Function</option>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	100 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	101 <conditional name="ggo">
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	102 <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	103 <when value="true">
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	104 <param name="level" type="select" label="Ontology level (the higher this number, the deeper the GO level, up to 3)">
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	105 <option value="1">1</option>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	106 <option value="2" selected="True">2</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	107 <option value="3">3</option>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	108 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	109 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	110 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	111 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	112 <conditional name="ego">
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	113 <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	114 <when value="true">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	115 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	116 <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	117 <conditional name="universe" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	118 <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	119 <when value="true">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	120 <conditional name="universe_input">
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	121 <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	122 <option value="text">Copy/paste your background IDs</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	123 <option value="file" selected="true">Input file containing your background IDs</option>
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	124 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	125 <when value="text" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	126 <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	127 <sanitizer>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	128 <valid initial="string.printable">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	129 <remove value="'"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	130 </valid>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	131 <mapping initial="none">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	132 <add source="'" target="__sq__"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	133 </mapping>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	134 </sanitizer>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	135 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	136 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	137 <when value="file" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	138 <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	139 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
9 2f67202ffdb3 planemo upload commit 6ca074d75447a272b570f7709ed10d0c8356bec5-dirty proteore parents: 8 diff changeset	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'>
2f67202ffdb3 planemo upload commit 6ca074d75447a272b570f7709ed10d0c8356bec5-dirty proteore parents: 8 diff changeset	141 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
2f67202ffdb3 planemo upload commit 6ca074d75447a272b570f7709ed10d0c8356bec5-dirty proteore parents: 8 diff changeset	142 </param>
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	143 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	144 </conditional>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	145 <conditional name="universe_idti" >
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	146 <param name="universe_idtypein" type="select" label="Select type of IDs of your background" help="" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	147 <option value="Uniprot">UniProt Accession number</option>
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	148 <option value="Entrez">Entrez Gene ID</option>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	149 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	150 <when value="Uniprot"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	151 <when value="Entrez"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	152 </conditional>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	153 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	154 <when value="false"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	155 </conditional>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	156 <param name="plot" type="select" display="checkboxes" multiple="true" label="Graphical display" optional="false">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	157 <option selected = "true" value="dotplot">dot-plot</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	158 <option value="barplot">bar-plot</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	159 </param>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	160 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	161 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	162 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	163 </inputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	164 <outputs>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	165 <data name="log" format="tsv" label="Cluster profiler" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	166 <collection type="list" label="clusterProfiler text files" name="text_output">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	167 <discover_datasets pattern="(?P<designation>.+\.tsv)" ext="tsv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	168 </collection>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	169 <collection type="list" label="clusterProfiler diagram outputs" name="graph_output" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	170 <discover_datasets pattern="(?P<designation>.+plot)" ext="png" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	171 </collection>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	172 </outputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	173 <tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	174 <test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	175 <conditional name="input">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	176 <param name="ids" value="file"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	177 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	178 <param name="header" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	179 <param name="ncol" value="c1"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	180 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	181 <conditional name="idti">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	182 <param name="idtypein" value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	183 </conditional>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	184 <param name="species" value="org.Hs.eg.db"/>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	185 <conditional name="ggo">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	186 <param name="go_represent" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	187 <param name="level" value="3"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	188 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	189 <conditional name="ego">
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	190 <param name="go_enrich" value="true"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	191 <conditional name="universe_input">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	192 <param name="universe_ids" value="file"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	193 <param name="file" value="background_ids.txt"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	194 <param name="header" value="true"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	195 <param name="ncol" value="c7"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	196 </conditional>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	197 <conditional name="universe_idti" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	198 <param name="universe_idtypein" value="Uniprot"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	199 </conditional>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	200 </conditional>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	201 <param name="ontology" value="CC,BP,MF"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	202 <param name="plot" value="dotplot,barplot"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	203 <output name="log" file="log.txt" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	204 <output_collection name="text_output">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	205 <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	206 <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	207 <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	208 <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	209 <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	210 <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	211 </output_collection>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	212 <output_collection name="graph_output">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	213 <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	214 <element name="GGO_BP_bar-plot" file="GGO_BP_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	215 <element name="GGO_MF_bar-plot" file="GGO_MF_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	216 <element name="EGO_CC_bar-plot" file="EGO_CC_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	217 <element name="EGO_BP_bar-plot" file="EGO_BP_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	218 <element name="EGO_CC_dot-plot" file="EGO_CC_dot-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	219 <element name="EGO_BP_dot-plot" file="EGO_BP_dot-plot" ftype="png"/>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	220 </output_collection>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	221 </test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	222 </tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	223 <help><![CDATA[
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	224
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	225 Description
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	226
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	227 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	228
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	229 Given a list of IDs, this tool:
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	230
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	231 (i) performs gene classification based on GO distribution at a specific level,
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	232
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	233 (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	234
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	235 -----
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	236
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	237 Input
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	238
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	239 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	240
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	241 "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.
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	242
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	243 .. class:: warningmark
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	244
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	245 In copy/paste mode, the number of IDs considered in input is limited to 5000.
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	246
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	247 -----
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	248
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	249 Parameters
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	250
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	251 "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	252
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	253 "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	254
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	255 "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	256
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	257 "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	258
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	259 "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	260
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	261 "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	262
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	263 "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	264
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	265 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	266
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	267 Of note: for Human species, you can build your own background by using the "Build tissue-specific expression dataset" tool of ProteoRE.
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4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	269 -----
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	270
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	271 Output
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	272
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	273 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	274 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.
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7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	276 -----
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	277
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	278 Authors
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	279
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	280 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	281 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	282
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	283 User manual / Documentation of the clusterProfiler R package (functions and parameters):
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	284 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	286 -----
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	287
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	288 .. class:: infomark
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	289
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	290 Bioconductor Packages used:
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	291
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	292 - bioconductor-org.hs.eg.db v3.5.0
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	293 - bioconductor-org.mm.eg.db v3.5.0
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	294 - bioconductor-org.rn.eg.db v3.5.0
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	295 - dose v3.2.0
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	296 - clusterprofiler v 3.4.4
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d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	298 .. class:: infomark
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	299
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	300 Galaxy integration
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	301
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	302 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	303
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	304 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	305
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	306 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	308 Help: contact@proteore.org for any questions or concerns about this tool.
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	309
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	310
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	311 ]]></help>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	312 <citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	313 </citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	314 </tool>

Mercurial > repos > proteore > proteore_clusterprofiler

annotate cluster_profiler.xml @ 10:d951677a50d4 draft