Mercurial > repos > proteore > proteore_prot_features
comparison prot_features.xml @ 2:6659a32876ea draft
planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
author | proteore |
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date | Tue, 27 Feb 2018 08:11:33 -0500 |
parents | bfc679370c64 |
children | 57657705cd70 |
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1:bfc679370c64 | 2:6659a32876ea |
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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 |