proteore_clusterprofiler: cluster

annotate cluster_profiler.xml @ 11:37370cab5e5f draft

planemo upload commit 3305e0bef3621ca618b08e9f2fa79e55ecd11595

author	proteore
date	Tue, 25 Sep 2018 05:12:32 -0400
parents	6604d9aa7cf3
children	7a5814f0392a

rev	line source
11 37370cab5e5f planemo upload commit 3305e0bef3621ca618b08e9f2fa79e55ecd11595 proteore parents: 10 diff changeset	1 <tool id="cluter_profiler" name="clusterProfiler" version="2018.09.25">
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	2 <description>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	3 GO terms classification and enrichment analysis
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	4 </description>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	5 <requirements>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	6 <requirement type="package" version="3.4.1">R</requirement>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	7 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	8 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
4 18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	9 <requirement type="package" version="3.5.0">bioconductor-org.Rn.eg.db</requirement>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	10 <requirement type="package" version="3.2.0">bioconductor-dose</requirement>
3 67a796154e2a planemo upload commit 07fb0efd8a1badeb395fa1dc435037998b4de25f proteore parents: 2 diff changeset	11 <requirement type="package" version="3.4.4">bioconductor-clusterprofiler</requirement>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	12 </requirements>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	13 <command detect_errors="exit_code"><![CDATA[
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	14 Rscript "$__tool_directory__/GO-enrich.R"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	15 #if $input.ids == "text"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	16 --input_type="text"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	17 --input="$input.txt"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	18 #else
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	19 --input_type="file"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	20 --input="$input.file"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	21 --ncol="$input.ncol"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	22 --header="$input.header"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	23 #end if
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	24
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	25 --id_type="$idti.idtypein"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	26
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	27 --species="$species"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	28
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	29 #if $ggo.go_represent == "true"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	30 --go_represent="true"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	31 --level="$ggo.level"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	32 #else
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	33 --go_represent="false"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	34 #end if
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	35
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	36 #if $ego.go_enrich == "true"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	37 --go_enrich="true"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	38 --pval_cutoff="$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
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	55
4 18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	56 --plot="$plot"
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	57 --onto_opt="$ontology" > $log
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	58 ]]></command>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	59 <inputs>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	60 <conditional name="input" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	61 <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list (Uniprot accession Nb or Entrez Gene ID) from a file (e.g. table)" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	62 <option value="text">Copy/paste your identifiers</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	63 <option value="file" selected="true">Input file containing your identifiers</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	64 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	65 <when value="text" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	66 <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	67 <sanitizer>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	68 <valid initial="string.printable">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	69 <remove value="'"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	70 </valid>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	71 <mapping initial="none">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	72 <add source="'" target="__sq__"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	73 </mapping>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	74 </sanitizer>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	75 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	76 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	77 <when value="file" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	78 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	79 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	80 <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	81 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	82 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	83 <conditional name="idti" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	84 <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	85 <option value="Uniprot">UniProt accession number (e.g. P31946)</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	86 <option value="Entrez">Entrez Gene ID (e.g : 4151)</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	87 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	88 <when value="Uniprot"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	89 <when value="Entrez"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	90 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	91
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	92 <param name="species" type="select" label="Select a species" >
2 1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty proteore parents: 1 diff changeset	93 <option value="org.Hs.eg.db">Human</option>
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty proteore parents: 1 diff changeset	94 <option value="org.Mm.eg.db">Mouse</option>
4 18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	95 <option value="org.Rn.eg.db">Rat</option>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	96 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	97 <conditional name="ggo">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	98 <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Do you want to perform GO categories representation analysis?"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	99 <when value="true">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	100 <param name="level" type="select" label="Level of the ontology at which the profile has to be built (the higher this number, the deeper the GO level)">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	101 <option value="1">1</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	102 <option value="2">2</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	103 <option value="3" selected="True">3</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	104 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	105 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	106 <when value="false"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	107 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	108 <conditional name="ego">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	109 <param name="go_enrich" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Do you want to perform GO categories enrichment analysis?"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	110 <when value="true">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	111 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	112 <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	113 <conditional name="universe" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	114 <param name="universe_option" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Would you like to define your own background IDs?"/>
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 <conditional name="universe_input">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	117 <param name="universe_ids" type="select" label="Provide your background IDs list" help="Copy/paste or ID list (Uniprot accession Nb or Entrez Gene ID) from a file (e.g. table)" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	118 <option value="text">Copy/paste your background identifiers</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	119 <option value="file" selected="true">Input file containing your background identifiers</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	120 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	121 <when value="text" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	122 <param name="txt" type="text" label="Copy/paste your background 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	123 <sanitizer>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	124 <valid initial="string.printable">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	125 <remove value="'"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	126 </valid>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	127 <mapping initial="none">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	128 <add source="'" target="__sq__"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	129 </mapping>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	130 </sanitizer>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	131 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	132 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	133 <when value="file" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	134 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your background IDs list" help="" />
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	135 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	136 <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	137 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	138 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	139 <conditional name="universe_idti" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	140 <param name="universe_idtypein" type="select" label="Select type/source of background identifier of your list" help="Please see example of IDs in help section" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	141 <option value="Uniprot">UniProt accession number</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	142 <option value="Entrez">Entrez Gene ID</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	143 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	144 <when value="Uniprot"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	145 <when value="Entrez"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	146 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	147 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	148 <when value="false"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	149 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	150 </when>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	151 <when value="false"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	152 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	153
4 18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	154 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category" optional="false">
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	155 <option value="CC">Cellular Component</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	156 <option value="BP">Biological Process</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	157 <option value="MF">Molecular Function</option>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	158 </param>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	159
4 18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	160 <param name="plot" type="select" display="checkboxes" multiple="true" label="Please select your visualization for enrichment analysis" optional="false">
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	161 <option selected = "true" value="dotplot">dot-plot</option>
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	162 <option value="barplot">bar-plot</option>
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	163 </param>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	164
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	165 </inputs>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	166 <outputs>
11 37370cab5e5f planemo upload commit 3305e0bef3621ca618b08e9f2fa79e55ecd11595 proteore parents: 10 diff changeset	167 <data name="log" format="tabular" label="Cluster profiler" />
4 18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	168 <collection type="list" label="clusterProfiler text files" name="text_output">
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	169 <discover_datasets pattern="(?P<designation>.+\.csv)" ext="csv"/>
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	170 </collection>
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	171 <collection type="list" label="clusterProfiler diagram outputs" name="graph_output" >
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	172 <discover_datasets pattern="(?P<designation>.+plot)" ext="png" />
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	173 </collection>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	174 </outputs>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	175 <tests>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	176 <test>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	177 <conditional name="input">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	178 <param name="ids" value="file"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	179 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	180 <param name="header" value="true"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	181 <param name="ncol" value="c1"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	182 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	183 <conditional name="idti">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	184 <param name="idtypein" value="Uniprot"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	185 </conditional>
5 36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	186 <param name="species" value="org.Hs.eg.db"/>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	187 <conditional name="ggo">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	188 <param name="go_represent" value="true"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	189 <param name="level" value="3"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	190 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	191 <conditional name="ego">
5 36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	192 <param name="go_enrich" value="true"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	193 <conditional name="universe_input">
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	194 <param name="universe_ids" value="file"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	195 <param name="file" value="background_ids.txt"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	196 <param name="header" value="true"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	197 <param name="ncol" value="c7"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	198 </conditional>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	199 <conditional name="universe_idti" >
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	200 <param name="universe_idtypein" value="Uniprot"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	201 </conditional>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	202 </conditional>
5 36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	203 <param name="ontology" value="CC,BP,MF"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	204 <param name="plot" value="dotplot,barplot"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	205 <output name="log" file="log.txt" />
4 18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty proteore parents: 3 diff changeset	206 <output_collection name="text_output">
5 36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	207 <element name="cluster_profiler_GGO_CC.csv" file="cluster_profiler_GGO_CC.csv" ftype="csv"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	208 <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_GGO_BP.csv" ftype="csv"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	209 <element name="cluster_profiler_GGO_MF.csv" file="cluster_profiler_GGO_MF.csv" ftype="csv"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	210 <element name="cluster_profiler_EGO_CC.csv" file="cluster_profiler_EGO_CC.csv" ftype="csv"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	211 <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_EGO_BP.csv" ftype="csv"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	212 <element name="cluster_profiler_EGO_MF.csv" file="cluster_profiler_EGO_MF.csv" ftype="csv"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	213
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	214 </output_collection>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	215 <output_collection name="graph_output">
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	216 <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png" diff="size"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	217 <element name="GGO_BP_bar-plot" file="GGO_BP_bar-plot" ftype="png" diff="size"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	218 <element name="GGO_MF_bar-plot" file="GGO_MF_bar-plot" ftype="png" diff="size"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	219 <element name="EGO_CC_bar-plot" file="EGO_CC_bar-plot" ftype="png" diff="size"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	220 <element name="EGO_BP_bar-plot" file="EGO_BP_bar-plot" ftype="png" diff="size"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	221 <element name="EGO_CC_dot-plot" file="EGO_CC_dot-plot" ftype="png" diff="size"/>
36c586c918eb planemo upload commit 654ba92763264fb669b084d7939700f8f1180217-dirty proteore parents: 4 diff changeset	222 <element name="EGO_BP_dot-plot" file="EGO_BP_dot-plot" ftype="png" diff="size"/>
0 076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	223 </output_collection>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	224 </test>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	225 </tests>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	226 <help><![CDATA[
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	227
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	228 Galaxy component based on R package clusterProfiler (see ref below)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	229
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	230 This component allows to perform GO enrichment-analyses.
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	231
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	232 Given a list of IDs, the tool either
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	233 (i) performs gene classification based on GO distribution at a specific level, or
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	234 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, compared to a background.
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	235 User has the possibility to use for this background: either the whole organism, or a user-defined list. In this latter case,
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	236 we recommand to use the "Retrieve tissue-specific expression data" ProteoRE tool to constitute this list according to user
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	237 parameters.
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	238
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	239 Input required
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	240
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	241 This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946).
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	242
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	243 Two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	244 or by copy/pasting your IDs (separated by a space).
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	245
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	246
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	247 Output
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	248
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	249 Text (tables) and graphics representing the repartition and/or enrichment of GO categories.
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	250
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	251 User manual / Documentation of the clusterProfiler R package (functions and parameters):
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	252 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	253 (Very well explained)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	254
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	255 Reference
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	256
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	257 clusterProfiler R package reference :
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	258 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	259 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287.
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	260 doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	261
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	262 -----
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	263
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	264 .. class:: infomark
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	265
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	266 Galaxy integration
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	267
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	268 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	269
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	270 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	271
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	272 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	273
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	274 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	275
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	276
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	277 ]]></help>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	278 <citations>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	279 </citations>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	280 </tool>

Mercurial > repos > proteore > proteore_clusterprofiler

annotate cluster_profiler.xml @ 11:37370cab5e5f draft