proteore_clusterprofiler: cluster

annotate cluster_profiler.xml @ 6:5e16cec55146 draft

planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty

author	proteore
date	Thu, 29 Mar 2018 11:43:28 -0400
parents	8a91f58782df
children	4609346d8108

rev	line source
2 a71792aa5a08 planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty proteore parents: 1 diff changeset	1 <tool id="cluter_profiler" name="clusterProfiler" version="0.1.0">
a71792aa5a08 planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty proteore parents: 1 diff changeset	2 <description>
a71792aa5a08 planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty proteore parents: 1 diff changeset	3 GO terms classification and enrichment analysis
a71792aa5a08 planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty proteore parents: 1 diff changeset	4 </description>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	5 <requirements>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	6 <requirement type="package" version="3.4.1">R</requirement>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	7 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	8 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	9 <requirement type="package" version="3.2.0">bioconductor-dose</requirement>
1 09ba28df72ad planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: 0 diff changeset	10 <requirement type="package" version="3.4.4">bioconductor-clusterprofiler</requirement>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	11 </requirements>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	12 <command detect_errors="exit_code"><![CDATA[
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	13 Rscript "$__tool_directory__/GO-enrich.R"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	14 #if $input.ids == "text"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	15 --input_type="text"
4 710414ebb6db planemo upload commit 0a42c3d46be24406936ca0036bb436e6e2524fd2-dirty proteore parents: 3 diff changeset	16 --input="$input.txt"
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	17 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	18 --input_type="file"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	19 --input="$input.file"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	20 --ncol="$input.ncol"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	21 --header="$input.header"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	22 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	23
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	24 --id_type="$idti.idtypein"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	25
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	26 --species="$species"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	27
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	28 #if $ggo.go_represent == "true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	29 --go_represent="true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	30 --level="$ggo.level"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	31 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	32 --go_represent="false"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	33 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	34
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	35 #if $ego.go_enrich == "true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	36 --go_enrich="true"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	37 --pval_cutoff="$ego.pval"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	38 --qval_cutoff="$ego.qval"
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	39 #if $ego.universe.universe_option == "true"
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	40 #if $ego.universe.universe_input.universe_ids == "text"
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	41 --universe_type="text"
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	42 --universe="$ego.universe.universe_input.txt"
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	43 #else
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	44 --universe_type="file"
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	45 --universe="$ego.universe.universe_input.file"
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	46 --uncol="$ego.universe.universe_input.ncol"
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	47 --uheader="$ego.universe.universe_input.header"
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	48 #end if
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	49 --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	50 #end if
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	51 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	52 --go_enrich="false"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	53 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	54
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	55 --onto_opt="$ontology"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	56
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	57 --text_output="$text_output"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	58 ]]></command>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	59 <inputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	60 <conditional name="input" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	61 <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	62 <option value="text">Copy/paste your identifiers</option>
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	63 <option value="file" selected="true">Input file containing your identifiers</option>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	64 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	65 <when value="text" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-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' >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	67 <sanitizer>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	68 <valid initial="string.printable">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	69 <remove value="'"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	70 </valid>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	71 <mapping initial="none">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	72 <add source="'" target="__sq__"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	73 </mapping>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	74 </sanitizer>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	75 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	76 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	77 <when value="file" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-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="" />
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	79 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
3 ad1244024bd8 planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty proteore parents: 2 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' />
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	81 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	82 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	83 <conditional name="idti" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-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" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	85 <option value="Uniprot">UniProt accession number</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	86 <option value="Entrez">Entrez Gene ID</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	87 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	88 <when value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	89 <when value="Entrez"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	90 </conditional>
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	91
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	92 <param name="species" type="select" label="Select a species" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	93 <option value="human">Human</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	94 <option value="mouse">Mouse</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	95 <option value="rat">Rat</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	96 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	97 <conditional name="ggo">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-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?"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	99 <when value="true">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-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)">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	101 <option value="1">1</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	102 <option value="2">2</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	103 <option value="3" selected="True">3</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	104 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	105 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	106 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	107 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	108 <conditional name="ego">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-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?"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	110 <when value="true">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	111 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	112 <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
6 5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	113 <conditional name="universe" >
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 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?"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	115 <when value="true">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	116 <conditional name="universe_input">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	117 <param name="universe_ids" type="select" label="Provide your background IDs list" help="Copy/paste or ID list from a file (e.g. table)" >
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	118 <option value="text">Copy/paste your background identifiers</option>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	119 <option value="file" selected="true">Input file containing your background identifiers</option>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	120 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	121 <when value="text" >
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 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' >
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	123 <sanitizer>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	124 <valid initial="string.printable">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	125 <remove value="'"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	126 </valid>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	127 <mapping initial="none">
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	128 <add source="'" target="__sq__"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	129 </mapping>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	130 </sanitizer>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	131 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	132 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	133 <when value="file" >
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	134 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your background IDs list" help="" />
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	135 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 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' />
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	137 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	138 </conditional>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	139 <conditional name="universe_idti" >
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 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" >
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	141 <option value="Uniprot">UniProt accession number</option>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	142 <option value="Entrez">Entrez Gene ID</option>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	143 </param>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	144 <when value="Uniprot"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	145 <when value="Entrez"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	146 </conditional>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	147 </when>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	148 <when value="false"/>
5e16cec55146 planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty proteore parents: 5 diff changeset	149 </conditional>
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	150 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	151 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	152 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	153
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	154 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	155 <option value="CC">Cellular Component</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	156 <option value="BP">Biological Process</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	157 <option value="MF">Molecular Function</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	158 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	159
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	160
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	161
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	162 </inputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	163 <outputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	164 <data name="text_output" format="tabular" label="clusterProfiler text output" />
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	165 <collection type="list" label="clusterProfiler diagram outputs" name="output" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	166 <discover_datasets pattern="(?P<designation>.+\.png)" ext="png" />
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	167 </collection>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	168 </outputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	169 <tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	170 <test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	171 <conditional name="input">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	172 <param name="ids" value="file"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	173 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	174 <param name="header" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	175 <param name="ncol" value="c1"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	176 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	177 <conditional name="idti">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	178 <param name="idtypein" value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	179 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	180 <param name="species" value="human"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	181 <conditional name="ggo">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	182 <param name="go_represent" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	183 <param name="level" value="3"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	184 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	185 <conditional name="ego">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	186 <param name="go_enrich" value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	187 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	188 <param name="ontology" value="CC"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	189 <output name="text_output" file="clusterProfiler_text_output.tabular"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	190 <output_collection name="output">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	191 <element name="clusterProfiler_diagram_outputs__GGO.CC.png" file="clusterProfiler_diagram_outputs__GGO.CC.png" ftype="png"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	192 </output_collection>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	193 </test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	194 </tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	195 <help><![CDATA[
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	196
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	197 Galaxy component based on R package clusterProfiler (see ref below)
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	198
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	199 This component allows to perform GO enrichment-analyses.
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	200
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	201 Given a list of IDs, the tool either
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	202 (i) performs gene classification based on GO distribution at a specific level, or
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	203 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, compared to a background (whole organism or user-defined list).
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	204
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	205 Input required
1 09ba28df72ad planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: 0 diff changeset	206
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	207 This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946).
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	208
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	209 Two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers)
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	210 or by copy/pasting your IDs (separated by a space).
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	211
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	212
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	213 Output
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	214
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	215 Text (tables) and graphics representing the repartition and/or enrichment of GO categories.
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	216
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	217 User manual / Documentation of the clusterProfiler R package (functions and parameters):
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	218 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	219 (Very well explained)
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	220
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	221 Reference
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	222
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	223 clusterProfiler R package reference :
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	224 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	225 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287.
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	226 doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	227
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	228 -----
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	229
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	230 .. class:: infomark
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	231
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	232 Galaxy integration
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	233
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	234 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	235
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	236 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	237
5 8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	238 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	239
8a91f58782df planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty proteore parents: 4 diff changeset	240 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	241
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	242
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	243 ]]></help>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	244 <citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	245 </citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	246 </tool>

Mercurial > repos > proteore > proteore_clusterprofiler

annotate cluster_profiler.xml @ 6:5e16cec55146 draft