proteore_clusterprofiler: cluster

annotate cluster_profiler.xml @ 42:3a990910e7f4 draft default tip

"planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty"

author	proteore
date	Fri, 09 Apr 2021 14:38:05 +0000
parents	3fd1ccc57a6a
children

rev	line source
42 3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	1 <tool id="cluter_profiler" name="Classification and enrichment analysis" version="2021.04.08">
29 52735594cd45 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9 proteore parents: 28 diff changeset	2 <description>(Human, Mouse, Rat)[clusterProfiler]</description>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	3 <requirements>
42 3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	4 <requirement type="package" version="4.0.3">r-base</requirement>
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	5 <requirement type="package" version="3.12.0">bioconductor-org.hs.eg.db</requirement>
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	6 <requirement type="package" version="3.12.0">bioconductor-org.mm.eg.db</requirement>
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	7 <requirement type="package" version="3.12.0">bioconductor-org.rn.eg.db</requirement>
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	8 <requirement type="package" version="1.52.0">bioconductor-annotationdbi</requirement>
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	9 <requirement type="package" version="3.16.0">bioconductor-dose</requirement>
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	10 <requirement type="package" version="3.18.1">bioconductor-clusterprofiler</requirement>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	11 </requirements>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	12 <command detect_errors="exit_code"><![CDATA[
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	13 Rscript "$__tool_directory__/GO-enrich.R"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	14 #if $input.ids == "text"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	15 --input_type="text"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	16 --input="$input.txt"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	17 #else
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	18 --input_type="file"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	19 --input="$input.file"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	20 --ncol="$input.ncol"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	21 --header="$input.header"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	22 #end if
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 diff changeset	23
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	24 --id_type="$idti.idtypein"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	25
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	26 --species="$species"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	27
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	28 #if $ggo.go_represent == "true"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	29 --go_represent="true"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	30 --level="$ggo.level"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	31 #else
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	32 --go_represent="false"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	33 #end if
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	34
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	35 #if $ego.go_enrich == "true"
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 diff changeset	36 --plot="$ego.plot"
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	37 --go_enrich="true"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	38 --pval_cutoff="$ego.pval"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	39 --qval_cutoff="$ego.qval"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	40 #if $ego.universe.universe_option == "true"
4 18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	41 #if $ego.universe.universe_input.universe_ids == "text"
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	42 --universe_type="text"
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	43 --universe="$ego.universe.universe_input.txt"
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	44 #else
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	45 --universe_type="file"
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	46 --universe="$ego.universe.universe_input.file"
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	47 --uncol="$ego.universe.universe_input.ncol"
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	48 --uheader="$ego.universe.universe_input.header"
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	49 #end if
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	50 --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	51 #end if
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	52 #else
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	53 --go_enrich="false"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	54 #end if
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 diff changeset	55
4 18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	56 --onto_opt="$ontology" > $log
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	57 ]]></command>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	58 <inputs>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	59 <conditional name="input" >
36 51d79e4496cc planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty proteore parents: 35 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)" >
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	61 <option value="text">Copy/paste your IDs</option>
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	62 <option value="file" selected="true">Input file containing your IDs</option>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	63 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	64 <when value="text" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-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' >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	66 <sanitizer>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	67 <valid initial="string.printable">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	68 <remove value="'"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	69 </valid>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	70 <mapping initial="none">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	71 <add source="'" target="__sq__"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	72 </mapping>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	73 </sanitizer>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	74 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	75 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	76 <when value="file" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-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="" />
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	78 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
32 f2c0a2b44841 planemo upload commit bfee528de437dc698b227a274983af3f3106cbb3-dirty proteore parents: 31 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'>
f2c0a2b44841 planemo upload commit bfee528de437dc698b227a274983af3f3106cbb3-dirty proteore parents: 31 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>
f2c0a2b44841 planemo upload commit bfee528de437dc698b227a274983af3f3106cbb3-dirty proteore parents: 31 diff changeset	81 </param>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	82 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	83 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	84 <conditional name="idti" >
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	85 <param name="idtypein" type="select" label="Select type/source of IDs" help="" >
36 51d79e4496cc planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty proteore parents: 35 diff changeset	86 <option value="Uniprot">UniProt accession number (e.g. P31946)</option>
51d79e4496cc planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty proteore parents: 35 diff changeset	87 <option value="Entrez">Entrez Gene ID (e.g. 4151)</option>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	88 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	89 <when value="Uniprot"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	90 <when value="Entrez"/>
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 diff changeset	91 </conditional>
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	92 <param name="species" type="select" label="Species" >
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	93 <option value="org.Hs.eg.db">Human (Homo sapiens) </option>
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	94 <option value="org.Mm.eg.db">Mouse (Mus musculus) </option>
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	95 <option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option>
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	96 </param>
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	97 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Select GO terms category" optional="false" >
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	98 <option value="CC">Cellular Component</option>
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	99 <option value="BP">Biological Process</option>
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	100 <option value="MF">Molecular Function</option>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	101 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	102 <conditional name="ggo">
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	103 <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Perform GO categories representation analysis?"/>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	104 <when value="true">
36 51d79e4496cc planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty proteore parents: 35 diff changeset	105 <param name="level" type="select" label="Ontology level (the higher this number, the deeper the GO level, up to 3)">
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	106 <option value="1">1</option>
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	107 <option value="2" selected="True">2</option>
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	108 <option value="3">3</option>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	109 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	110 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	111 <when value="false"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	112 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	113 <conditional name="ego">
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	114 <param name="go_enrich" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Perform GO categories enrichment analysis?"/>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	115 <when value="true">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	116 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	117 <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	118 <conditional name="universe" >
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	119 <param name="universe_option" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Define your own background IDs?"/>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	120 <when value="true">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	121 <conditional name="universe_input">
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 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)" >
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	123 <option value="text">Copy/paste your background IDs</option>
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	124 <option value="file" selected="true">Input file containing your background IDs</option>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	125 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	126 <when value="text" >
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 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' >
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	128 <sanitizer>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	129 <valid initial="string.printable">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	130 <remove value="'"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	131 </valid>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	132 <mapping initial="none">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	133 <add source="'" target="__sq__"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	134 </mapping>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	135 </sanitizer>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	136 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	137 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	138 <when value="file" >
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	139 <param name="file" type="data" format="txt,tabular" label="Select file that contains your background IDs list" help="" />
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	140 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
32 f2c0a2b44841 planemo upload commit bfee528de437dc698b227a274983af3f3106cbb3-dirty proteore parents: 31 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'>
f2c0a2b44841 planemo upload commit bfee528de437dc698b227a274983af3f3106cbb3-dirty proteore parents: 31 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>
f2c0a2b44841 planemo upload commit bfee528de437dc698b227a274983af3f3106cbb3-dirty proteore parents: 31 diff changeset	143 </param>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	144 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	145 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	146 <conditional name="universe_idti" >
36 51d79e4496cc planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty proteore parents: 35 diff changeset	147 <param name="universe_idtypein" type="select" label="Select type of IDs of your background" help="" >
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	148 <option value="Uniprot">UniProt Accession number</option>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	149 <option value="Entrez">Entrez Gene ID</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	150 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	151 <when value="Uniprot"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	152 <when value="Entrez"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	153 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	154 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	155 <when value="false"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	156 </conditional>
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	157 <param name="plot" type="select" display="checkboxes" multiple="true" label="Graphical display" optional="false">
22 6dafa28110f5 planemo upload commit f9fa23f3f9cefa5c4a3dc06686add83a23c17ad0-dirty proteore parents: 21 diff changeset	158 <option selected = "true" value="dotplot">dot-plot</option>
6dafa28110f5 planemo upload commit f9fa23f3f9cefa5c4a3dc06686add83a23c17ad0-dirty proteore parents: 21 diff changeset	159 <option value="barplot">bar-plot</option>
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	160 </param>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	161 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	162 <when value="false"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	163 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	164 </inputs>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	165 <outputs>
28 eafb37258a6f planemo upload commit 62db30a8a6c62c0106fda053ca75eb48e90ea705-dirty proteore parents: 27 diff changeset	166 <data name="log" format="tsv" label="Cluster profiler" />
4 18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	167 <collection type="list" label="clusterProfiler text files" name="text_output">
20 a91d407e1938 planemo upload commit d636fd65b39353cbb29228d309235f3a6db37568-dirty proteore parents: 19 diff changeset	168 <discover_datasets pattern="(?P<designation>.+\.tsv)" ext="tsv"/>
4 18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	169 </collection>
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	170 <collection type="list" label="clusterProfiler diagram outputs" name="graph_output" >
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	171 <discover_datasets pattern="(?P<designation>.+plot)" ext="png" />
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	172 </collection>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	173 </outputs>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	174 <tests>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	175 <test>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	176 <conditional name="input">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	177 <param name="ids" value="file"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	178 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	179 <param name="header" value="true"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	180 <param name="ncol" value="c1"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	181 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	182 <conditional name="idti">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	183 <param name="idtypein" value="Uniprot"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	184 </conditional>
5 36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	185 <param name="species" value="org.Hs.eg.db"/>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	186 <conditional name="ggo">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	187 <param name="go_represent" value="true"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	188 <param name="level" value="3"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	189 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	190 <conditional name="ego">
5 36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	191 <param name="go_enrich" value="true"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	192 <conditional name="universe_input">
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	193 <param name="universe_ids" value="file"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	194 <param name="file" value="background_ids.txt"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	195 <param name="header" value="true"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	196 <param name="ncol" value="c7"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	197 </conditional>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	198 <conditional name="universe_idti" >
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	199 <param name="universe_idtypein" value="Uniprot"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	200 </conditional>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	201 </conditional>
5 36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	202 <param name="ontology" value="CC,BP,MF"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	203 <param name="plot" value="dotplot,barplot"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	204 <output name="log" file="log.txt" />
4 18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	205 <output_collection name="text_output">
42 3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	206 <element name="cluster_profiler_GGO_CC.tsv" file="cluster_profiler_GGO_CC.csv" ftype="tsv"/>
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	207 <!--- <element name="cluster_profiler_GGO_BP.tsv" file="cluster_profiler_GGO_BP.csv" ftype="tsv"/> -->
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	208 <element name="cluster_profiler_GGO_MF.tsv" file="cluster_profiler_GGO_MF.csv" ftype="tsv"/>
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	209 <element name="cluster_profiler_EGO_CC.tsv" file="cluster_profiler_EGO_CC.csv" ftype="tsv"/>
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	210 <element name="cluster_profiler_EGO_BP.tsv" file="cluster_profiler_GGO_BP.csv" ftype="tsv"/>
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	211 <element name="cluster_profiler_EGO_MF.tsv" file="cluster_profiler_EGO_MF.csv" ftype="tsv"/>
5 36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	212 </output_collection>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	213 <output_collection name="graph_output">
31 b62fd03a3822 planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty proteore parents: 30 diff changeset	214 <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png"/>
b62fd03a3822 planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty proteore parents: 30 diff changeset	215 <element name="GGO_BP_bar-plot" file="GGO_BP_bar-plot" ftype="png"/>
b62fd03a3822 planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty proteore parents: 30 diff changeset	216 <element name="GGO_MF_bar-plot" file="GGO_MF_bar-plot" ftype="png"/>
b62fd03a3822 planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty proteore parents: 30 diff changeset	217 <element name="EGO_CC_bar-plot" file="EGO_CC_bar-plot" ftype="png"/>
b62fd03a3822 planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty proteore parents: 30 diff changeset	218 <element name="EGO_BP_bar-plot" file="EGO_BP_bar-plot" ftype="png"/>
b62fd03a3822 planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty proteore parents: 30 diff changeset	219 <element name="EGO_CC_dot-plot" file="EGO_CC_dot-plot" ftype="png"/>
b62fd03a3822 planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty proteore parents: 30 diff changeset	220 <element name="EGO_BP_dot-plot" file="EGO_BP_dot-plot" ftype="png"/>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	221 </output_collection>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	222 </test>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	223 </tests>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	224 <help><![CDATA[
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	225
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	226 Description
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	227
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 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).
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	229
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 diff changeset	230 Given a list of IDs, this tool:
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	231
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	232 (i) performs gene classification based on GO distribution at a specific level,
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 diff changeset	233
3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 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.
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	235
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	236 -----
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	237
31 b62fd03a3822 planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty proteore parents: 30 diff changeset	238 Input
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	239
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 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).
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	241
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 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.
36 51d79e4496cc planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty proteore parents: 35 diff changeset	243
51d79e4496cc planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty proteore parents: 35 diff changeset	244 .. class:: warningmark
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 diff changeset	245
36 51d79e4496cc planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty proteore parents: 35 diff changeset	246 In copy/paste mode, the number of IDs considered in input is limited to 5000.
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	247
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	248 -----
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	249
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	250 Parameters
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	251
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 diff changeset	252 "Species": the three supported species are Homo sapiens, Mus musculus and Rattus norvegicus
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	253
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 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")
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	255
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 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.
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	257
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	258 "Perform GO categories enrichment analysis?": calculate enrichment test for GO terms based on hypergeometric distribution (set to "Yes")
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	259
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	260 "P-value cut off": P-value threshold value for the declaration of significance (default is < 0.01)
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	261
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 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)
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	263
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 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 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	265
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 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.
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	267
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 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.
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	269
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 diff changeset	270 -----
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	271
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	272 Output
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	273
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 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.
3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 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.
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30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	277 -----
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	278
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	279 Authors
36 51d79e4496cc planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty proteore parents: 35 diff changeset	280
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 diff changeset	281 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
30 eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 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)
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	283
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	284 User manual / Documentation of the clusterProfiler R package (functions and parameters):
eb12bb18b5dd planemo upload commit 8b5a5b0b634bf3f62913a06a936c6f7295fa9f2b proteore parents: 29 diff changeset	285 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
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076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	287 -----
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	288
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	289 .. class:: infomark
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	290
39 3d4cdea0ea20 planemo upload commit 9664cb97c1ab9d21af2b302eb976015178089a72 proteore parents: 37 diff changeset	291 Bioconductor Packages used:
36 51d79e4496cc planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty proteore parents: 35 diff changeset	292
42 3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	293 - bioconductor-org.hs.eg.db v3.12.0
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	294 - bioconductor-org.mm.eg.db v3.12.0
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	295 - bioconductor-org.rn.eg.db v3.12.0
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	296 - dose v3.16.0
3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	297 - clusterprofiler v 3.18.1
34 f078633d9669 planemo upload commit a172073d58a2fc713af8656d3bcfa28592dcc242-dirty proteore parents: 33 diff changeset	298
f078633d9669 planemo upload commit a172073d58a2fc713af8656d3bcfa28592dcc242-dirty proteore parents: 33 diff changeset	299 .. class:: infomark
f078633d9669 planemo upload commit a172073d58a2fc713af8656d3bcfa28592dcc242-dirty proteore parents: 33 diff changeset	300
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	301 Galaxy integration
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	302
36 51d79e4496cc planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty proteore parents: 35 diff changeset	303 Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	304
42 3a990910e7f4 "planemo upload commit be9070db4a3b178ab45ecd9c9c3ab369240f7617-dirty" proteore parents: 41 diff changeset	305 Christophe Caron, Valentin Loux - INRAE, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	306
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	307 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	308
36 51d79e4496cc planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty proteore parents: 35 diff changeset	309 Help: contact@proteore.org for any questions or concerns about this tool.
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	310
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	311
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	312 ]]></help>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	313 <citations>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	314 </citations>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	315 </tool>

Mercurial > repos > proteore > proteore_clusterprofiler

annotate cluster_profiler.xml @ 42:3a990910e7f4 draft default tip