proteore_clusterprofiler: cluster

annotate cluster_profiler.xml @ 2:a71792aa5a08 draft

planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty

author	proteore
date	Wed, 07 Mar 2018 09:37:57 -0500
parents	09ba28df72ad
children	ad1244024bd8

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 $input.ids == "text"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	15 --input_type="text"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	16 --input="$input.text"
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="$ego.qval"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	39 #else
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	40 --go_enrich="false"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	41 #end if
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	42
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	43 --onto_opt="$ontology"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	44
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	45 --text_output="$text_output"
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	46 ]]></command>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	47 <inputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	48 <conditional name="input" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	49 <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	50 <option value="text">Copy/paste your identifiers</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	51 <option value="file">Input file containing your identifiers</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	52 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	53 <when value="text" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	54 <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	55 <sanitizer>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	56 <valid initial="string.printable">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	57 <remove value="'"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	58 </valid>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	59 <mapping initial="none">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	60 <add source="'" target="__sq__"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	61 </mapping>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	62 </sanitizer>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	63 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	64 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	65 <when value="file" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	66 <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	67 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	68 <param name="ncol" type="text" 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' />
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	69 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	70 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	71 <conditional name="idti" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	72 <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	73 <option value="Uniprot">UniProt accession number</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	74 <option value="Entrez">Entrez Gene ID</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	75 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	76 <when value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	77 <when value="Entrez"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	78 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	79 <param name="species" type="select" label="Select a species" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	80 <option value="human">Human</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	81 <option value="mouse">Mouse</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	82 <option value="rat">Rat</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	83 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	84 <conditional name="ggo">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	85 <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	86 <when value="true">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	87 <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	88 <option value="1">1</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	89 <option value="2">2</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	90 <option value="3" selected="True">3</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	91 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	92 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	93 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	94 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	95 <conditional name="ego">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	96 <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	97 <when value="true">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	98 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	99 <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	100 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	101 <when value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	102 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	103 <!--conditional name="fun" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	104 <param name="go_function" type="select" display="checkboxes" multiple="true" label="Please select analyses to perform">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	105 <option value="ggo">GO categories representation</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	106 <option value="ego">GO categories enrichment (compared to a background/reference)</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	107 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	108 <when value="ggo" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	109 <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	110 <option value="1">1</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	111 <option value="2">2</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	112 <option value="3" selected="True">3</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	113 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	114 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	115 <when value="ego" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	116 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	117 <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	118 </when>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	119 </conditional-->
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	120
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	121 <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	122 <option value="CC">Cellular Component</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	123 <option value="BP">Biological Process</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	124 <option value="MF">Molecular Function</option>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	125 </param>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	126
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	127
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	128
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	129 </inputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	130 <outputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	131 <data name="text_output" format="tabular" label="clusterProfiler text output" />
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	132 <collection type="list" label="clusterProfiler diagram outputs" name="output" >
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	133 <discover_datasets pattern="(?P<designation>.+\.png)" ext="png" />
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	134 </collection>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	135 </outputs>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	136 <tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	137 <test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	138 <conditional name="input">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	139 <param name="ids" value="file"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	140 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	141 <param name="header" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	142 <param name="ncol" value="c1"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	143 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	144 <conditional name="idti">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	145 <param name="idtypein" value="Uniprot"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	146 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	147 <param name="species" value="human"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	148 <conditional name="ggo">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	149 <param name="go_represent" value="true"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	150 <param name="level" value="3"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	151 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	152 <conditional name="ego">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	153 <param name="go_enrich" value="false"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	154 </conditional>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	155 <param name="ontology" value="CC"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	156 <output name="text_output" file="clusterProfiler_text_output.tabular"/>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	157 <output_collection name="output">
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	158 <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	159 </output_collection>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	160 </test>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	161 </tests>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	162 <help><![CDATA[
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	163
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	164 Galaxy component based on R package clusterProfiler (see ref below)
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	165
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	166 This component allows to perform GO enrichment-analyses.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	167 Given a list of IDs, the tool either
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	168 (i) performs gene classification based on GO distribution at a specific level, or
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	169 (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list,
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	170 compared to a background (whole organism or user-defined list).
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	171
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	172 Input required
1 09ba28df72ad planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: 0 diff changeset	173
0 bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	174 This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946).
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	175 You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) where there are contained.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	176
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	177
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	178 Output
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	179
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	180 Text (tables) and graphics representing the repartition and/or enrichment of GO categories.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	181
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	182 User manual / Documentation of the clusterProfiler R package (functions and parameters):
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	183 https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	184 (Very well explained)
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	185
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	186 Reference
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	187
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	188 clusterProfiler R package reference :
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	189 G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	190 OMICS: A Journal of Integrative Biology 2012, 16(5):284-287.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	191 doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	192
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	193
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	194 Galaxy integration
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	195
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	196 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	197
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	198 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	199
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	200 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	201
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	202 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	203
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	204
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	205 ]]></help>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	206 <citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	207 </citations>
bd052861852b planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty proteore parents: diff changeset	208 </tool>

Mercurial > repos > proteore > proteore_clusterprofiler

annotate cluster_profiler.xml @ 2:a71792aa5a08 draft