proteore_clusterprofiler: cluster

annotate cluster_profiler.xml @ 13:f6107b8ae8f8 draft default tip

"planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty"

author	proteore
date	Fri, 09 Apr 2021 14:39:05 +0000
parents	85f039f53414
children

rev	line source
13 f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	1 <tool id="cluter_profiler" name="Classification and enrichment analysis" version="2021.04.08">
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>
13 f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	4 <requirement type="package" version="4.0.3">r-base</requirement>
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	5 <requirement type="package" version="3.12.0">bioconductor-org.hs.eg.db</requirement>
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	6 <requirement type="package" version="3.12.0">bioconductor-org.mm.eg.db</requirement>
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	7 <requirement type="package" version="3.12.0">bioconductor-org.rn.eg.db</requirement>
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	8 <requirement type="package" version="1.52.0">bioconductor-annotationdbi</requirement>
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	9 <requirement type="package" version="3.16.0">bioconductor-dose</requirement>
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	10 <requirement type="package" version="3.18.1">bioconductor-clusterprofiler</requirement>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	11 </requirements>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	12 <command detect_errors="exit_code"><![CDATA[
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	13 Rscript "$__tool_directory__/GO-enrich.R"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	14 #if $input.ids == "text"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	15 --input_type="text"
4 710414ebb6db planemo upload commit 0a42c3d46be24406936ca0036bb436e6e2524fd2-dirty proteore parents: 3 diff changeset	16 --input="$input.txt"
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	17 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	18 --input_type="file"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	19 --input="$input.file"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	20 --ncol="$input.ncol"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	21 --header="$input.header"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	22 #end if
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	23
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	24 --id_type="$idti.idtypein"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	25
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	26 --species="$species"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	27
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	28 #if $ggo.go_represent == "true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	29 --go_represent="true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	30 --level="$ggo.level"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	31 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	32 --go_represent="false"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	33 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	34
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	35 #if $ego.go_enrich == "true"
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	36 --plot="$ego.plot"
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	37 --go_enrich="true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	38 --pval_cutoff="$ego.pval"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	39 --qval_cutoff="$ego.qval"
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	40 #if $ego.universe.universe_option == "true"
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	41 #if $ego.universe.universe_input.universe_ids == "text"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	42 --universe_type="text"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	43 --universe="$ego.universe.universe_input.txt"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	44 #else
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	45 --universe_type="file"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	46 --universe="$ego.universe.universe_input.file"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	47 --uncol="$ego.universe.universe_input.ncol"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	48 --uheader="$ego.universe.universe_input.header"
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	49 #end if
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	50 --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	51 #end if
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	52 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	53 --go_enrich="false"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	54 #end if
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	55
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	56 --onto_opt="$ontology" > $log
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	57 ]]></command>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	58 <inputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	59 <conditional name="input" >
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	60 <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	61 <option value="text">Copy/paste your IDs</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	62 <option value="file" selected="true">Input file containing your IDs</option>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	63 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	64 <when value="text" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	65 <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	66 <sanitizer>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	67 <valid initial="string.printable">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	68 <remove value="'"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	69 </valid>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	70 <mapping initial="none">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	71 <add source="'" target="__sq__"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	72 </mapping>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	73 </sanitizer>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	74 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	75 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	76 <when value="file" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	77 <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	78 <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	79 <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	80 <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	81 </param>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	82 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	83 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	84 <conditional name="idti" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	85 <param name="idtypein" type="select" label="Select type/source of IDs" help="" >
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	86 <option value="Uniprot">UniProt accession number (e.g. P31946)</option>
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	87 <option value="Entrez">Entrez Gene ID (e.g. 4151)</option>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	88 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	89 <when value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	90 <when value="Entrez"/>
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	91 </conditional>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	92 <param name="species" type="select" label="Species" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	93 <option value="org.Hs.eg.db">Human (Homo sapiens) </option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	94 <option value="org.Mm.eg.db">Mouse (Mus musculus) </option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	95 <option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	96 </param>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	97 <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	98 <option value="CC">Cellular Component</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	99 <option value="BP">Biological Process</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	100 <option value="MF">Molecular Function</option>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	101 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	102 <conditional name="ggo">
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	103 <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	104 <when value="true">
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	105 <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	106 <option value="1">1</option>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	107 <option value="2" selected="True">2</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	108 <option value="3">3</option>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	109 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	110 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	111 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	112 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	113 <conditional name="ego">
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	114 <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	115 <when value="true">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	116 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	117 <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	118 <conditional name="universe" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	119 <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	120 <when value="true">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	121 <conditional name="universe_input">
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	122 <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	123 <option value="text">Copy/paste your background IDs</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	124 <option value="file" selected="true">Input file containing your background IDs</option>
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	125 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	126 <when value="text" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	127 <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	128 <sanitizer>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	129 <valid initial="string.printable">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	130 <remove value="'"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	131 </valid>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	132 <mapping initial="none">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	133 <add source="'" target="__sq__"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	134 </mapping>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	135 </sanitizer>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	136 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	137 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	138 <when value="file" >
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	139 <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	140 <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	141 <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	142 <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	143 </param>
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	144 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	145 </conditional>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	146 <conditional name="universe_idti" >
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	147 <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	148 <option value="Uniprot">UniProt Accession number</option>
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	149 <option value="Entrez">Entrez Gene ID</option>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	150 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	151 <when value="Uniprot"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	152 <when value="Entrez"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	153 </conditional>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	154 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	155 <when value="false"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	156 </conditional>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	157 <param name="plot" type="select" display="checkboxes" multiple="true" label="Graphical display" optional="false">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	158 <option selected = "true" value="dotplot">dot-plot</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	159 <option value="barplot">bar-plot</option>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	160 </param>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	161 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	162 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	163 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	164 </inputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	165 <outputs>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	166 <data name="log" format="tsv" label="Cluster profiler" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	167 <collection type="list" label="clusterProfiler text files" name="text_output">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	168 <discover_datasets pattern="(?P<designation>.+\.tsv)" ext="tsv"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	169 </collection>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	170 <collection type="list" label="clusterProfiler diagram outputs" name="graph_output" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	171 <discover_datasets pattern="(?P<designation>.+plot)" ext="png" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	172 </collection>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	173 </outputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	174 <tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	175 <test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	176 <conditional name="input">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	177 <param name="ids" value="file"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	178 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	179 <param name="header" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	180 <param name="ncol" value="c1"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	181 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	182 <conditional name="idti">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	183 <param name="idtypein" value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	184 </conditional>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	185 <param name="species" value="org.Hs.eg.db"/>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	186 <conditional name="ggo">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	187 <param name="go_represent" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	188 <param name="level" value="3"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	189 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	190 <conditional name="ego">
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	191 <param name="go_enrich" value="true"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	192 <conditional name="universe_input">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	193 <param name="universe_ids" value="file"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	194 <param name="file" value="background_ids.txt"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	195 <param name="header" value="true"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	196 <param name="ncol" value="c7"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	197 </conditional>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	198 <conditional name="universe_idti" >
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	199 <param name="universe_idtypein" value="Uniprot"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	200 </conditional>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	201 </conditional>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	202 <param name="ontology" value="CC,BP,MF"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	203 <param name="plot" value="dotplot,barplot"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	204 <output name="log" file="log.txt" />
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	205 <output_collection name="text_output">
13 f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	206 <element name="cluster_profiler_GGO_CC.tsv" file="cluster_profiler_GGO_CC.csv" ftype="tsv"/>
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	207 <!--- <element name="cluster_profiler_GGO_BP.tsv" file="cluster_profiler_GGO_BP.csv" ftype="tsv"/> -->
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	208 <element name="cluster_profiler_GGO_MF.tsv" file="cluster_profiler_GGO_MF.csv" ftype="tsv"/>
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	209 <element name="cluster_profiler_EGO_CC.tsv" file="cluster_profiler_EGO_CC.csv" ftype="tsv"/>
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	210 <element name="cluster_profiler_EGO_BP.tsv" file="cluster_profiler_GGO_BP.csv" ftype="tsv"/>
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	211 <element name="cluster_profiler_EGO_MF.tsv" file="cluster_profiler_EGO_MF.csv" ftype="tsv"/>
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	212 </output_collection>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	213 <output_collection name="graph_output">
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	214 <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	215 <element name="GGO_BP_bar-plot" file="GGO_BP_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	216 <element name="GGO_MF_bar-plot" file="GGO_MF_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	217 <element name="EGO_CC_bar-plot" file="EGO_CC_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	218 <element name="EGO_BP_bar-plot" file="EGO_BP_bar-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	219 <element name="EGO_CC_dot-plot" file="EGO_CC_dot-plot" ftype="png"/>
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	220 <element name="EGO_BP_dot-plot" file="EGO_BP_dot-plot" ftype="png"/>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	221 </output_collection>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	222 </test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	223 </tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	224 <help><![CDATA[
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	225
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	226 Description
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	227
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	228 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	229
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	230 Given a list of IDs, this tool:
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	231
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	232 (i) performs gene classification based on GO distribution at a specific level,
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	233
cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	234 (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.
7 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
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	238 Input
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	239
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	240 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	241
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	242 "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.
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	243
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	244 .. class:: warningmark
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	245
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	246 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	247
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	248 -----
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	249
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	250 Parameters
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	251
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	252 "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	253
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	254 "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	255
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	256 "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	257
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	258 "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	259
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	260 "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	261
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	262 "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	263
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	264 "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	265
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	266 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.
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	267
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	268 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	269
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	270 -----
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	271
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	272 Output
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	273
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	274 Diagram output: graphical output in the form of bar-plot or dot-plot (png, jpeg or pdf format), one figure for each GO category.
cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	275 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	276
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	277 -----
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	278
7 4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	279 Authors
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	280
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	281 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	282 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	283
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	284 User manual / Documentation of the clusterProfiler R package (functions and parameters):
4609346d8108 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba proteore parents: 6 diff changeset	285 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	287 -----
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	288
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	289 .. class:: infomark
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	290
11 cc2bd0d2afa2 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 10 diff changeset	291 Bioconductor Packages used:
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	292
13 f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	293 - bioconductor-org.hs.eg.db v3.12.0
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	294 - bioconductor-org.mm.eg.db v3.12.0
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	295 - bioconductor-org.rn.eg.db v3.12.0
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	296 - dose v3.16.0
f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	297 - clusterprofiler v 3.18.1
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	298
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	299 .. class:: infomark
d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	300
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	301 Galaxy integration
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	302
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	303 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	304
13 f6107b8ae8f8 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 12 diff changeset	305 Christophe Caron, Valentin Loux - INRAE, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	306
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	307 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	308
10 d951677a50d4 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty proteore parents: 9 diff changeset	309 Help: contact@proteore.org for any questions or concerns about this tool.
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	310
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bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	312 ]]></help>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	313 <citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	314 </citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	315 </tool>

Mercurial > repos > proteore > proteore_clusterprofiler

annotate cluster_profiler.xml @ 13:f6107b8ae8f8 draft default tip