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comparison reactome_analysis.xml @ 1:8200968789c1 draft

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planemo upload commit 1b95e5bc85662f10cdd6305587ccee8faf9a2354-dirty
author proteore
date Fri, 07 Dec 2018 10:43:57 -0500
parents 19d8daa1eb2e
children db63d069b5e6
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0:19d8daa1eb2e 1:8200968789c1
1 <tool id="reactome_analysis" name="Reactome" version="2018.10.12"> 1 <tool id="reactome_analysis" name="Reactome" version="2018.12.07">
2 <description>display your protein list on the Reactome pathway browser</description> 2 <description>display your protein list on the Reactome pathway browser</description>
3 <requirements> 3 <requirements>
4 </requirements> 4 </requirements>
5 <stdio> 5 <stdio>
6 <exit_code range="1:" /> 6 <exit_code range="1:" />
7 </stdio> 7 </stdio>
8 <command><![CDATA[ 8 <command><![CDATA[
9
10 python $__tool_directory__/reactome_analysis.py
9 #if $opt.input == "text" 11 #if $opt.input == "text"
10 python $__tool_directory__/reactome_analysis.py --json "$opt.list" "list" --output "$output" --trash "$trash" 12 --json "$opt.list" "list"
11 #else if $opt.input == "file" 13 #else if $opt.input == "file"
12 python $__tool_directory__/reactome_analysis.py --json "$opt.file" "file" $opt.header $opt.ncol --output "$output" --trash "$trash" 14 --json "$opt.file" "file" "$opt.header" "$opt.ncol"
13 #end if 15 #end if
16 --output "$output"
17 --trash "$trash"
18 --species "$species"
14 19
15 ]]></command> 20 ]]></command>
16 <inputs> 21 <inputs>
17 <conditional name="opt"> 22 <conditional name="opt">
18 <param name="input" type="select" label="Input identifiers (Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157) or gene name (e.g. AQP7)" multiple="False" > 23 <param name="input" type="select" label="Input identifiers (Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157) or gene name (e.g. AQP7)" multiple="False" >
34 <when value="file" > 39 <when value="file" >
35 <param name="file" type="data" format="txt, tabular" label="Input file containing your identifiers" help="Input file is a tab-delimited file with at least one contain containing identifier" /> 40 <param name="file" type="data" format="txt, tabular" label="Input file containing your identifiers" help="Input file is a tab-delimited file with at least one contain containing identifier" />
36 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> 41 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
37 <param type="text" name="ncol" value="c1" label="Please specify the column number where are your IDs (e.g : Enter c1 for column n°1)" /> 42 <param type="text" name="ncol" value="c1" label="Please specify the column number where are your IDs (e.g : Enter c1 for column n°1)" />
38 </when> 43 </when>
39
40 </conditional> 44 </conditional>
45 <param name="species" type="select" label="Select species">
46 <option value="48887">Human (H. sapiens)</option>
47 <option value="48892">Mouse (M. musculus)</option>
48 <option value="48895">Rat (R. norvegicus)</option>
49 </param>
41 </inputs> 50 </inputs>
42 <outputs> 51 <outputs>
43 <data name="output" format="html" label="" /> 52 <data name="output" format="html" label="" />
44 <data name="trash" format="tabular" hidden="true" label="Invalid id not send to reactome"> 53 <data name="trash" format="tabular" hidden="true" label="Invalid id not send to reactome">
45 <discover_datasets pattern="(Reactome_Analysis_Tools_invalid_ID).txt" ext="tabular" visible="false" assign_primary_output="false"/> 54 <discover_datasets pattern="(Reactome_Analysis_Tools_invalid_ID).txt" ext="tabular" visible="false" assign_primary_output="false"/>
62 71
63 **For the rows that have more than 1 ID, only the first one is taken into account.** 72 **For the rows that have more than 1 ID, only the first one is taken into account.**
64 73
65 **Supported IDs: Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157), gene name (e.g. AQP7). If there is any ID containing invalid characters, it will be removed from the queue and placed in "Invalid identifiers" file.** 74 **Supported IDs: Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157), gene name (e.g. AQP7). If there is any ID containing invalid characters, it will be removed from the queue and placed in "Invalid identifiers" file.**
66 75
76 **Supported species: Human (H. sapiens), Mouse (M. musculus), Rat (Rattus norvegicus)**
77
67 ----- 78 -----
68 79
69 .. class:: infomark 80 .. class:: infomark
70 81
71 **Authors** 82 **Authors**