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comparison prot_features.xml @ 2:6659a32876ea draft

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planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
author proteore
date Tue, 27 Feb 2018 08:11:33 -0500
parents bfc679370c64
children 57657705cd70
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1:bfc679370c64 2:6659a32876ea
1 <tool id="prot_features" name="Protein Features (neXtProt)" version="0.1.0"> 1 <tool id="prot_features" name="Protein Features (neXtProt)" version="0.1.0">
2 <description> 2 <description>
3 Annotate your protein list using features retrieved from neXtProt database. 3 Annotate your protein list using features retrieved from neXtProt database.
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="3.4.1">R</requirement>
6 </requirements> 7 </requirements>
7 <stdio> 8 <stdio>
8 <exit_code range="1:" /> 9 <exit_code range="1:" />
9 </stdio> 10 </stdio>
10 <command><![CDATA[ 11 <command><![CDATA[
11 12
12 #if $inputtype.filetype == "copy_paste": 13 #if $inputtype.filetype == "copy_paste":
13 14
14 Rscript $__tool_directory__/protein_features.R --inputtype=copypaste --input='$inputtype.genelist' --nextprot=$__tool_directory__/result_nextprot.txt --column=c1 --argsP1='$Nextprot_params.P1' --argsP2='$Nextprot_params.P2' --argsP3='$Nextprot_params.P3' --type='$idtype' --output='$output' --header=None 15 Rscript $__tool_directory__/protein_features.R
16 --inputtype=copypaste
17 --input='$inputtype.genelist'
18 --nextprot=$__tool_directory__/tool-data/result_nextprot.txt
19 --column=c1 --header=None
20 --argsP1='$Nextprot_params.P1'
21 --argsP2='$Nextprot_params.P2'
22 --argsP3='$Nextprot_params.P3'
23 --type='$idtype'
24 --output='$output'
15 25
16 #end if 26 #end if
17 27
18 #if $inputtype.filetype == "file_all": 28 #if $inputtype.filetype == "file_all":
19 29
20 Rscript $__tool_directory__/protein_features.R --inputtype=tabfile --input='$inputtype.genelist' --nextprot=$__tool_directory__/result_nextprot.txt --column='$inputtype.column' --argsP1='$Nextprot_params.P1' --argsP2='$Nextprot_params.P2' --argsP3='$Nextprot_params.P3' --type='$idtype' --output='$output' --header='$inputtype.header' 30 Rscript $__tool_directory__/protein_features.R
31 --inputtype=tabfile
32 --input='$inputtype.genelist'
33 --nextprot=$__tool_directory__/tool-data/result_nextprot.txt
34 --column='$inputtype.column' --header='$inputtype.header'
35 --argsP1='$Nextprot_params.P1'
36 --argsP2='$Nextprot_params.P2'
37 --argsP3='$Nextprot_params.P3'
38 --type='$idtype'
39 --output='$output'
21 40
22 #end if 41 #end if
23 42
24 ]]></command> 43 ]]></command>
25 44
110 129
111 The output is a tabular file. The initial columns are kept and columns are be added according to which annotation you have selected. 130 The output is a tabular file. The initial columns are kept and columns are be added according to which annotation you have selected.
112 131
113 **Authors** 132 **Authors**
114 133
115 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 134 Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
116 135
117 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform 136 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
118 137
119 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 138 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
120 139