proteore_goprofiles: goprofiles.xml annotate

annotate goprofiles.xml @ 8:386145573c19 draft

planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b

author	proteore
date	Tue, 18 Dec 2018 09:54:57 -0500
parents	6afe8166a9a4
children	948fecb6a40b

rev	line source
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	1 <tool id="goProfiles" name="Statistical analysis of functional profiles" version="2018.12.12">
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	2 <description>(Human, Mouse) [goProfiles]</description>
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	3 <requirements>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	4 <requirement type="package" version="3.4.1">R</requirement>
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	6 <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	7 <!--requirement type="package" version="3.5.0">bioconductor-org.rn.eg.db</requirement-->
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	8 <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	9 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	10 <requirement type="package" version="1.38.0">goprofiles</requirement>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	11 </requirements>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	12 <stdio>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	13 <exit_code range="1:" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	14 </stdio>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	15 <command><![CDATA[
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	16 Rscript $__tool_directory__/goprofiles.R
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	17 #if $input.ids == "text"
1 1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	18 --input_type="text"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	19 --input="$input.text"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	20 #else
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	21 --input_type="file"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	22 --input="$input.file"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	23 --ncol="$input.ncol"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	24 --header="$input.header"
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	25 #end if
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	26
1 1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	27 --id_type="$input.id_type"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	28 --onto_opt="$onto_opt"
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	29 --plot_opt="$plot_opt"
1 1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	30 --level="$level"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	31 --per="$per"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	32 --title="$title"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	33 --duplicate="$duplicate"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	34 --text_output="$text_output"
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	35 --species="$species" > $log
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	36
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	37 ]]></command>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	38 <inputs>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	39 <conditional name="input" >
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	40 <param name="ids" type="select" label="Enter your IDs (Entrez Gene ID or UniProt Accession number)" help="Copy/paste or from a file (e.g. table)" >
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	41 <option value="text">Copy/paste your IDs</option>
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	42 <option value="file" selected="true">Input file containing your IDs</option>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	43 </param>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	44 <when value="text" >
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	45 <param name="text" type="text" label="Copy/paste your IDs" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	46 <sanitizer>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	47 <valid initial="string.printable">
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	48 <remove value="'"/>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	49 </valid>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	50 <mapping initial="none">
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	51 <add source="'" target="__sq__"/>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	52 </mapping>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	53 </sanitizer>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	54 </param>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	55 <param name="id_type" type="select" label="Select type of IDs list" >
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	56 <option value="Entrez">Entrez Gene ID</option>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	57 <option value="UniProt">UniProt Accession number</option>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	58 </param>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	59 </when>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	60 <when value="file" >
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	61 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	62 <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	63 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	64 <param name="id_type" type="select" label="Select type of IDs list" >
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	65 <option value="Entrez">Entrez Gene ID</option>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	66 <option value="UniProt">Uniprot Accession number</option>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	67 </param>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	68 </when>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	69 </conditional>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	70 <param name="duplicate" type="boolean" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" />
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	71 <param name="species" type="select" label="Species">
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	72 <option value="org.Hs.eg.db">Human (Homo sapiens)</option>
781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	73 <option value="org.Mm.eg.db">Mouse (Mus musculus)</option>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	74 <!--option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option-->
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	75 </param>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	76 <param type="select" name="onto_opt" label="Select GO terms category" multiple="True" display="checkboxes" optional="false" >
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	77 <option value="CC">Cellular Component (CC)</option>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	78 <option value="MF">Molecular Function (MF)</option>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	79 <option value="BP">Biological Process (BP)</option>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	80 </param>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	81 <param type="select" name="level" label="Ontology level (the higher this number, the deeper the GO level)" >
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	82 <option value="1">1</option>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	83 <option value="2" selected="True">2</option>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	84 <option value="3">3</option>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	85 </param>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	86 <param type="boolean" name="per" label="Plot absolute frequencies?" truevalue="TRUE" falsevalue="FALSE" />
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	87 <param type="text" name="title" label="Enter title of your figure" />
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	88 <param type="select" name="plot_opt" label="Plot file format">
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	89 <option value="PNG">png</option>
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	90 <option value="JPEG">jpeg</option>
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	91 <option value="PDF" selected="True">pdf</option>
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	92 </param>
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	93
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	94 </inputs>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	95 <outputs>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	96 <data name="log" format="tsv" label="goProfiles log" />
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	97 <collection type="list" label="goProfiles text files" name="text_output">
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	98 <discover_datasets pattern="(?P<designation>.+\.tsv)" ext="tsv"/>
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	99 </collection>
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	100 <collection type="list" label="goProfiles diagram output" name="output" >
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	101 <discover_datasets pattern="(?P<designation>.+\.png)" ext="png" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	102 <discover_datasets pattern="(?P<designation>.+\.jpeg)" ext="jpg" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	103 <discover_datasets pattern="(?P<designation>.+\.pdf)" ext="pdf" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	104 </collection>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	105 </outputs>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	106 <tests>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	107 <test>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	108 <conditional name="input">
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	109 <param name="ids" value="file" />
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	110 <param name="file" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" />
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	111 <param name="ncol" value="c1" />
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	112 <param name="header" value="true" />
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	113 <param name="id_type" value="UniProt" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	114 </conditional>
1 1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	115 <param name="duplicate" value="false"/>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	116 <param name="onto_opt" value="CC,MF,BP" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	117 <param name="level" value="2" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	118 <param name="per" value="true" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	119 <param name="title" value="Test" />
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	120 <param name="plot_opt" value="PDF" />
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	121 <output_collection name="output" type="list" >
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	122 <element name="profile.BP.pdf" file="profile.BP.pdf" ftype="pdf" compare="sim_size"/>
781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	123 <element name="profile.CC.pdf" file="profile.CC.pdf" ftype="pdf" compare="sim_size"/>
781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	124 <element name="profile.MF.pdf" file="profile.MF.pdf" ftype="pdf" compare="sim_size"/>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	125 </output_collection>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	126 <output name="log" file="GO_Profile_text_output.tsv"/>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	127 </test>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	128 </tests>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	129 <help><![CDATA[
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	130
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	131 Description
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	132
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	133 This tool is based on the goProfiles R package; it performs statistical analysis of functional profiles based on Gene Ontology (GO). Functional profile at a given GO level is obtained by counting the
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	134 number of identifiers having a hit in each category of this level.
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	135
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	136 -----
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	137
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	138 Input
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	139
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	140 Two modes are allowed: either by copy/pasting your IDs (separated by a space) or by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers).
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	141 Only entrez gene ID (e.g : 4151) or Uniprot accession number (e.g. P31946) are allowed. If your list is not in this form, please use the ID_Converter tool of ProteoRE.
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	142
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	143 -----
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	144
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	145 Parameters
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	146
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	147 "Species": enter the sepcies you are working on; Homo sapiens and Mus musculus supported (Rattus norvegicus coming soon)
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	148
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	149 "Select GO terms category": you can choose one or more GO categories which are Biological Process (BP), Cellular Component (CC) and Molecular Function (MF)
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	150
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	151 "Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 3). In general the higher the level, the more semantically specific the term is.
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	152
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	153 -----
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	154
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	155 Ouput
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	156
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	157 Diagram output: graphical output in the form of bar-plot or dot-plot (png, jpeg or pdf format), one figure for each GO category.
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	158
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	159 text output: with the following information GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) and GO term frequency (e.g. BP.Frequency)
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	160
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	161 -----
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	162
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	163 .. class:: infomark
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	164
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	165 Authors
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	166
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	167 Salicrú M, Ocaña J, Sánchez-Pla A. Comparison of lists of genes based on functional profiles. BMC Bioinformatics. 2011. 12:401. doi:10.1186/1471-2105-12-401. PubMed PMID: 21999355
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	168
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	169 -----
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	170
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	171 .. class:: infomark
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	172
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	173 Galaxy integration
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	174
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	175 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	176
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	177 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform, FR
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	178
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	179 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	180
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	181 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	182
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	183 ]]></help>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	184 <citations>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	185 </citations>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	186 </tool>

Mercurial > repos > proteore > proteore_goprofiles

annotate goprofiles.xml @ 8:386145573c19 draft