proteore_clusterprofiler: cluster

annotate cluster_profiler.xml @ 2:1c98865a8508 draft

planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty

author	proteore
date	Wed, 05 Sep 2018 03:50:36 -0400
parents	91b9b48d07b3
children	67a796154e2a

rev	line source
2 1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty proteore parents: 1 diff changeset	1 <tool id="cluter_profiler" name="clusterProfiler" version="2018.09.04">
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>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	9 <requirement type="package" version="3.2.0">bioconductor-dose</requirement>
2 1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty proteore parents: 1 diff changeset	10 <requirement type="package" version="3.6.0">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="$input.header"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	22 #end if
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	23
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	24 --id_type="$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 $ego.go_enrich == "true"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	36 --go_enrich="true"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	37 --pval_cutoff="$ego.pval"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	38 --qval_cutoff="$ego.qval"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	39 #if $ego.universe.universe_option == "true"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	40 #if $ego.universe.universe_input.universe_ids == "text"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	41 --universe_type="text"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	42 --universe="$ego.universe.universe_input.txt"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	43 #else
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	44 --universe_type="file"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	45 --universe="$ego.universe.universe_input.file"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	46 --uncol="$ego.universe.universe_input.ncol"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	47 --uheader="$ego.universe.universe_input.header"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	48 #end if
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	49 --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	50 #end if
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	51 #else
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	52 --go_enrich="false"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	53 #end if
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	54
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	55 --onto_opt="$ontology"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	56
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	57 --text_output="$text_output"
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>
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty proteore parents: 1 diff changeset	95 <!--option value="org.Sc.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
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	154 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category">
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
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	160
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	161
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	162 </inputs>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	163 <outputs>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	164 <data name="text_output" format="tabular" label="clusterProfiler text output" />
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	165 <collection type="list" label="clusterProfiler diagram outputs" name="output" >
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	166 <discover_datasets pattern="(?P<designation>.+\.png)" ext="png" />
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	167 </collection>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	168 </outputs>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	169 <tests>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	170 <test>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	171 <conditional name="input">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	172 <param name="ids" value="file"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	173 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	174 <param name="header" value="true"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	175 <param name="ncol" value="c1"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	176 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	177 <conditional name="idti">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	178 <param name="idtypein" value="Uniprot"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	179 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	180 <param name="species" value="human"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	181 <conditional name="ggo">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	182 <param name="go_represent" value="true"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	183 <param name="level" value="3"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	184 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	185 <conditional name="ego">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	186 <param name="go_enrich" value="false"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	187 </conditional>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	188 <param name="ontology" value="CC"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	189 <output name="text_output" file="clusterProfiler_text_output.tabular"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	190 <output_collection name="output">
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	191 <element name="GGO.CC.png" file="GGO.CC.png" ftype="png"/>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	192 </output_collection>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	193 </test>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	194 </tests>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	195 <help><![CDATA[
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	196
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	197 Galaxy component based on R package clusterProfiler (see ref below)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	198
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	199 This component allows to perform GO enrichment-analyses.
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	200
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	201 Given a list of IDs, the tool either
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	202 (i) performs gene classification based on GO distribution at a specific level, or
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	203 (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	204 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	205 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	206 parameters.
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	207
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	208 Input required
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	209
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	210 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	211
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	212 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	213 or by copy/pasting your IDs (separated by a space).
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	214
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	215
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	216 Output
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	217
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	218 Text (tables) and graphics representing the repartition and/or enrichment of GO categories.
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	219
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	220 User manual / Documentation of the clusterProfiler R package (functions and parameters):
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	221 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	222 (Very well explained)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	223
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	224 Reference
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	225
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	226 clusterProfiler R package reference :
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	227 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	228 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287.
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	229 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	230
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	231 -----
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	232
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	233 .. class:: infomark
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	234
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	235 Galaxy integration
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	236
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	237 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	238
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	239 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	240
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	241 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	242
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	243 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	244
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	245
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	246 ]]></help>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	247 <citations>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	248 </citations>
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty proteore parents: diff changeset	249 </tool>

Mercurial > repos > proteore > proteore_clusterprofiler

annotate cluster_profiler.xml @ 2:1c98865a8508 draft