proteore_goprofiles: goprofiles.xml annotate

annotate goprofiles.xml @ 10:2138e0035e57 draft

planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty

author	proteore
date	Mon, 04 Mar 2019 08:20:52 -0500
parents	948fecb6a40b
children	3ddc1f78773d

rev	line source
10 2138e0035e57 planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty proteore parents: 9 diff changeset	1 <tool id="goProfiles" name="Statistical analysis of functional profiles" version="2019.02.27.1">
8 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>
9 948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	11
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	12 </requirements>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	13 <stdio>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	14 <exit_code range="1:" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	15 </stdio>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	16 <command><![CDATA[
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	17 Rscript $__tool_directory__/goprofiles.R
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	18 #if $input.ids == "text"
1 1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	19 --input_type="text"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	20 --input="$input.text"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	21 #else
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	22 --input_type="file"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	23 --input="$input.file"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	24 --ncol="$input.ncol"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	25 --header="$input.header"
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	26 #end if
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	27
1 1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	28 --id_type="$input.id_type"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	29 --onto_opt="$onto_opt"
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	30 --plot_opt="$plot_opt"
1 1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	31 --level="$level"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	32 --per="$per"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	33 --title="$title"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	34 --duplicate="$duplicate"
1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	35 --text_output="$text_output"
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	36 --species="$species" > $log
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	37
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	38 ]]></command>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	39 <inputs>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	40 <conditional name="input" >
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	41 <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	42 <option value="text">Copy/paste your IDs</option>
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	43 <option value="file" selected="true">Input file containing your IDs</option>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	44 </param>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	45 <when value="text" >
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	46 <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	47 <sanitizer>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	48 <valid initial="string.printable">
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	49 <remove value="'"/>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	50 </valid>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	51 <mapping initial="none">
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	52 <add source="'" target="__sq__"/>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	53 </mapping>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	54 </sanitizer>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	55 </param>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	56 <param name="id_type" type="select" label="Select type of IDs list" >
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	57 <option value="Entrez">Entrez Gene ID</option>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	58 <option value="UniProt">UniProt Accession number</option>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	59 </param>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	60 </when>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	61 <when value="file" >
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	62 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
9 948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	63 <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'>
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	64 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	65 </param>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	66 <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	67 <param name="id_type" type="select" label="Select type of IDs list" >
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	68 <option value="Entrez">Entrez Gene ID</option>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	69 <option value="UniProt">Uniprot Accession number</option>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	70 </param>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	71 </when>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	72 </conditional>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	73 <param name="duplicate" type="boolean" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" />
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	74 <param name="species" type="select" label="Species">
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	75 <option value="org.Hs.eg.db">Human (Homo sapiens)</option>
781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	76 <option value="org.Mm.eg.db">Mouse (Mus musculus)</option>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	77 <!--option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option-->
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	78 </param>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	79 <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	80 <option value="CC">Cellular Component (CC)</option>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	81 <option value="MF">Molecular Function (MF)</option>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	82 <option value="BP">Biological Process (BP)</option>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	83 </param>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	84 <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	85 <option value="1">1</option>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	86 <option value="2" selected="True">2</option>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	87 <option value="3">3</option>
9 948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	88 <option value="4">4</option>
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	89 <option value="5">5</option>
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	90 <option value="6">6</option>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	91 </param>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	92 <param type="boolean" name="per" label="Plot absolute frequencies?" truevalue="TRUE" falsevalue="FALSE" />
9 948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	93 <param type="text" name="title" label="Enter title of your figure">
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	94 <sanitizer invalid_char=''>
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	95 <valid initial="string.printable">
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	96 <remove value="'"/>
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	97 <remove value="/"/>
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	98 </valid>
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	99 <mapping>
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	100 <add source=" " target=""/>
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	101 </mapping>
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	102 </sanitizer>
948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	103 </param>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	104 <param type="select" name="plot_opt" label="Plot file format">
9 948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	105 <option value="PNG" selected="True">png</option>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	106 <option value="JPEG">jpeg</option>
9 948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	107 <option value="PDF">pdf</option>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	108 </param>
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	109
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	110 </inputs>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	111 <outputs>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	112 <data name="log" format="tsv" label="goProfiles log" />
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	113 <collection type="list" label="goProfiles text files" name="text_output">
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	114 <discover_datasets pattern="(?P<designation>.+\.tsv)" ext="tsv"/>
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	115 </collection>
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	116 <collection type="list" label="goProfiles diagram output" name="output" >
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	117 <discover_datasets pattern="(?P<designation>.+\.png)" ext="png" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	118 <discover_datasets pattern="(?P<designation>.+\.jpeg)" ext="jpg" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	119 <discover_datasets pattern="(?P<designation>.+\.pdf)" ext="pdf" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	120 </collection>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	121 </outputs>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	122 <tests>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	123 <test>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	124 <conditional name="input">
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	125 <param name="ids" value="file" />
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	126 <param name="file" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" />
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	127 <param name="ncol" value="c1" />
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	128 <param name="header" value="true" />
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	129 <param name="id_type" value="UniProt" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	130 </conditional>
1 1236ee08ccb8 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	131 <param name="duplicate" value="false"/>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	132 <param name="onto_opt" value="CC,MF,BP" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	133 <param name="level" value="2" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	134 <param name="per" value="true" />
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	135 <param name="title" value="Test" />
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	136 <param name="plot_opt" value="PDF" />
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	137 <output_collection name="output" type="list" >
5 781072a65600 planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty proteore parents: 4 diff changeset	138 <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	139 <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	140 <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	141 </output_collection>
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	142 <output name="log" file="GO_Profile_text_output.tsv"/>
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	143 </test>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	144 </tests>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	145 <help><![CDATA[
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	146
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	147 Description
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	148
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	149 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	150 number of identifiers having a hit in each category of this level.
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	151
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	152 -----
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	153
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	154 Input
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	155
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	156 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	157 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	158
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	159 -----
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	160
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	161 Parameters
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	162
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	163 "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	164
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	165 "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	166
9 948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	167 "Ontology level (the higher this number, the deeper the GO level)": correspond to the level of GO hierarchy (from 1 to 6). In general the higher the level, the more semantically specific the term is.
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	168
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	169 -----
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	170
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	171 Ouput
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	172
9 948fecb6a40b planemo upload commit 973d782455fd6a7df7ba9bce0a7878de53bc1e68-dirty proteore parents: 8 diff changeset	173 Diagram output: graphical output in the form of bar-plot or dot-plot (png (default format), jpeg or pdf format), one figure for each GO category.
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	174
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	175 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	176
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	177 -----
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	178
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	179 .. class:: infomark
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	180
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	181 Authors
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	182
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	183 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	184
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	185 -----
0 d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	186
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	187 .. class:: infomark
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	188
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	189 Galaxy integration
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	190
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	191 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	192
8 386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	193 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	194
386145573c19 planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b proteore parents: 6 diff changeset	195 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	196
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	197 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	198
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	199 ]]></help>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	200 <citations>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	201 </citations>
d89c09253c8d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty proteore parents: diff changeset	202 </tool>

Mercurial > repos > proteore > proteore_goprofiles

annotate goprofiles.xml @ 10:2138e0035e57 draft