Mercurial > repos > proteore > proteore_reactome

annotate reactome_analysis.xml @ 2:6c84a41c44d8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty
author proteore
date Wed, 07 Mar 2018 09:32:11 -0500
parents 35cd50b8ccf2
children be06c14e543d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
6c84a41c44d8 planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty
proteore
parents: 1
diff changeset
1 <tool id="reactome_analysis" name="Reactome" version="0.1.0">
6c84a41c44d8 planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty
proteore
parents: 1
diff changeset
2 <description>queries web service and display pathways
0
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
3 </description>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
4 <requirements>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
5 </requirements>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
6 <stdio>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
7 <exit_code range="1:" />
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
8 </stdio>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
9 <command><![CDATA[
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
10 #if $opt.input == "text"
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
11 python $__tool_directory__/reactome_analysis.py --json "$opt.list" "list" --output "$output" --trash "$trash"
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
12 #else if $opt.input == "file"
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
13 python $__tool_directory__/reactome_analysis.py --json "$opt.file" "file" $opt.header $opt.ncol --output "$output" --trash "$trash"
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
14 #end if
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
15
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
16 ]]></command>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
17 <inputs>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
18 <conditional name="opt">
1
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
19 <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" >
0
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
20 <option value="text">Copy/paste your list of IDs </option>
1
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
21 <option value="file">Input file containing your identifiers</option>
0
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
22 </param>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
23 <when value="text" >
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
24 <param name="list" type="text" label="Enter list of identifiers" />
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
25 </when>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
26 <when value="file" >
1
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
27 <param name="file" type="data" format="txt, tabular" label="Input file containing your identifiers" help="Input file is a tab-delimited file containing different information of proteins, such as an output of MaxQuant software" />
0
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
28 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
29 <param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' />
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
30 </when>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
31
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
32 </conditional>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
33 </inputs>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
34 <outputs>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
35 <data name="output" format="html" label="" />
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
36 <data name="trash" format="tabular" label="Invalid identifiers" />
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
37 </outputs>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
38 <tests>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
39 <test>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
40 <conditional name="opt" >
1
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
41 <param name="input" value="file" />
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
42 <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
43 <param name="header" value="true" />
0
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
44 <param name="ncol" value="c1" />
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
45 </conditional>
1
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
46 <output name="output" file="Reactome_Analysis_Tools.html" ftype="html" />
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
47 <output name="trash" file="Reactome_Analysis_Tools_invalid_ID.txt" ftype="tab" />
0
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
48 </test>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
49 </tests>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
50 <help><![CDATA[
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
51 Reactome software provides service of creating diagram representing the relations between the biological processes. This tool allows linking to Reactome web service with pre-loaded data from a list of IDs, a file containing IDs or from a column of a complexed file.
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
52
2
6c84a41c44d8 planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty
proteore
parents: 1
diff changeset
53 **For the rows that have more than 1 ID, only the first one is taken into account.**
6c84a41c44d8 planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty
proteore
parents: 1
diff changeset
54
6c84a41c44d8 planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty
proteore
parents: 1
diff changeset
55 **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.**
0
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
56
1
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
57 -----
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
58
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
59 .. class:: infomark
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
60
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
61 **Authors**
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
62
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
63 Fabregat et al. 2017 PMID: 29145629 (https://www.ncbi.nlm.nih.gov/pubmed/29145629)
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
64
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
65 Milacic et al. 2012 PMID:24213504 (https://www.ncbi.nlm.nih.gov/pubmed/24243840)
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
66
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
67 .. class:: infomark
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
68
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
69 **Galaxy integration**
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
70
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
71 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
72
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
73 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform,
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
74
35cd50b8ccf2 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents: 0
diff changeset
75 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
0
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
76 ]]></help>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
77 <citations>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
78 </citations>
216bd2a75b1d planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff changeset
79 </tool>