Mercurial > repos > proteore > proteore_maps_visualization

annotate kegg_maps_visualization.xml @ 3:f4938e47f2f8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 5e13878e9679f3f5ba8e482b9108249a43f3355e-dirty
author proteore
date Tue, 18 Dec 2018 09:38:13 -0500
parents 8a6863adcd09
children 4cc2265d1294
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
f4938e47f2f8 planemo upload commit 5e13878e9679f3f5ba8e482b9108249a43f3355e-dirty
proteore
parents: 2
diff changeset
1 <tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2018.12.18.1">
1
48f302ae5545 planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
proteore
parents: 0
diff changeset
2 <description>of (differentially expressed) genes/proteins</description>
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
3 <requirements>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
4 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
5 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
6 </requirements>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
8 Rscript $__tool_directory__/kegg_maps_visualization.R
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
9 #if $input.ids == "text"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
10 --id_list="$input.txt"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
11 #else
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
12 --input="$input.file"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
13 --id_column="$input.ncol"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
14 --header="$input.header"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
15 #end if
3
f4938e47f2f8 planemo upload commit 5e13878e9679f3f5ba8e482b9108249a43f3355e-dirty
proteore
parents: 2
diff changeset
16 #if $species.pathways.pathways_id != "pathways_file"
f4938e47f2f8 planemo upload commit 5e13878e9679f3f5ba8e482b9108249a43f3355e-dirty
proteore
parents: 2
diff changeset
17 --pathways_id="$species.pathways.pids"
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
18 #else
3
f4938e47f2f8 planemo upload commit 5e13878e9679f3f5ba8e482b9108249a43f3355e-dirty
proteore
parents: 2
diff changeset
19 --pathways_input="$species.pathways.file"
f4938e47f2f8 planemo upload commit 5e13878e9679f3f5ba8e482b9108249a43f3355e-dirty
proteore
parents: 2
diff changeset
20 --header2="$species.pathways.header2"
f4938e47f2f8 planemo upload commit 5e13878e9679f3f5ba8e482b9108249a43f3355e-dirty
proteore
parents: 2
diff changeset
21 --pathway_col="$species.pathways.ncol2"
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
22 #end if
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
23 --id_type="$id_type"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
24 --native_kegg="$native"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
25
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
26
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
27 #if $input.ids=="file" and $input.foldchange.fc=="true"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
28 --fold_change_data="$input.foldchange.fc"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
29 --fold_change_col="$input.foldchange.fc_col"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
30 #else
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
31 --fold_change_data="false"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
32 #end if
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
33
3
f4938e47f2f8 planemo upload commit 5e13878e9679f3f5ba8e482b9108249a43f3355e-dirty
proteore
parents: 2
diff changeset
34 --species=${species.ref_file}
f4938e47f2f8 planemo upload commit 5e13878e9679f3f5ba8e482b9108249a43f3355e-dirty
proteore
parents: 2
diff changeset
35 --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] }
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
36 --output="$text_output"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
37
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
38 ]]></command>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
39 <inputs>
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
40 <!--section name="pathways_section" title="Pathways" expanded="True"-->
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
41 <conditional name="species">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
42 <param name="ref_file" type="select" label="Species" >
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
43 <option value="hsa">Human (Homo sapiens)</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
44 <option value="mmu">Mouse (Mus musculus)</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
45 <option value="rno">Rat (Rattus norvegicus)</option>
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
46 </param>
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
47 <when value="hsa">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
48 <conditional name="pathways">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
49 <param name="pathways_id" type="select" label="Enter your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
50 <option value="pathways_names">KEGG pathway name(s)</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
51 <option value="pathways_ids">KEGG pathway IDs</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
52 <option value="pathways_file">KEGG pathway IDs from file</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
53 </param>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
54 <when value="pathways_names">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
55 <param name="pids" type="select" label="Select pathway(s) (by clicking in the box)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
56 <options from_data_table="hsa_pathways">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
57 <filter type="sort_by" column="1"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
58 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
59 </options>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
60 </param>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
61 </when>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
62 <when value="pathways_ids">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
63 <param name="pids" type="text" label="Copy/paste your pathway IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
64 <sanitizer invalid_char=''>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
65 <valid initial="string.printable">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
66 <remove value="&apos;"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
67 </valid>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
68 <mapping>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
69 <add source="&#x20;" target=""/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
70 </mapping>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
71 </sanitizer>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
72 </param>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
73 </when>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
74 <when value="pathways_file">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
75 <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
76 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
77 <param name="ncol2" type="text" value="c1" label="Column of pathways IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
78 </when>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
79 </conditional>
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
80 </when>
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
81 <when value="mmu">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
82 <conditional name="pathways">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
83 <param name="pathways_id" type="select" label="Enter your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
84 <option value="pathways_names">KEGG pathway name(s)</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
85 <option value="pathways_ids">KEGG pathway IDs</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
86 <option value="pathways_file">KEGG pathway IDs from file</option>
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
87 </param>
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
88 <when value="pathways_names">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
89 <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
90 <options from_data_table="mmu_pathways">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
91 <filter type="sort_by" column="1"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
92 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
93 </options>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
94 </param>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
95 </when>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
96 <when value="pathways_ids">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
97 <param name="pids" type="text" label="Copy/paste your pathway IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: "mmu00053 mmu00340"'>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
98 <sanitizer invalid_char=''>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
99 <valid initial="string.printable">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
100 <remove value="&apos;"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
101 </valid>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
102 <mapping>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
103 <add source="&#x20;" target=""/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
104 </mapping>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
105 </sanitizer>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
106 </param>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
107 </when>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
108 <when value="pathways_file">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
109 <param name="file" type="data" format="txt,tabular" label="Enter your file" help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" />
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
110 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
111 <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
112 </when>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
113 </conditional>
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
114 </when>
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
115 <when value="rno">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
116 <conditional name="pathways">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
117 <param name="pathways_id" type="select" label="Enter your pathway(s) name/id" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
118 <option value="pathways_names">KEGG pathway name(s)</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
119 <option value="pathways_ids">KEGG pathway IDs</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
120 <option value="pathways_file">KEGG pathway IDs from file</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
121 </param>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
122 <when value="pathways_names">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
123 <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
124 <options from_data_table="rno_pathways">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
125 <filter type="sort_by" column="1"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
126 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
127 </options>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
128 </param>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
129 </when>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
130 <when value="pathways_ids">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
131 <param name="pids" type="text" label="Copy/paste your pathway IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
132 <sanitizer invalid_char=''>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
133 <valid initial="string.printable">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
134 <remove value="&apos;"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
135 </valid>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
136 <mapping>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
137 <add source="&#x20;" target=""/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
138 </mapping>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
139 </sanitizer>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
140 </param>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
141 </when>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
142 <when value="pathways_file">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
143 <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
144 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
145 <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
146 </when>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
147 </conditional>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
148 </when>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
149 </conditional>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
150 <!--/section-->
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
151 <!--section name="genes_section" title="Genes/prot" expanded="True"-->
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
152 <param name="id_type" type="select" label="Select ID type for genes to map to the pathway(s):">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
153 <option value="geneID" selected="true">Entrez Gene ID</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
154 <option value="keggid">KEGG Genes ID</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
155 <option value="uniprotID">UniProt Accession number</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
156 </param>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
157 <conditional name="input" >
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
158 <param name="ids" type="select" label="Enter your IDs" help="Copy/paste or ID from file (e.g. table)" >
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
159 <option value="text">Copy/paste your IDs</option>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
160 <option value="file" selected="true">Input file containing your IDs</option>
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
161 </param>
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
162 <when value="text" >
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
163 <param name="txt" type="text" label="Copy/paste your IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: P31946 P62258' >
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
164 <sanitizer invalid_char=''>
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
165 <valid initial="string.printable">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
166 <remove value="&apos;"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
167 </valid>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
168 <mapping initial="none">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
169 <add source="&apos;" target="__sq__"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
170 </mapping>
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
171 </sanitizer>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
172 </param>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
173 </when>
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
174 <when value="file" >
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
175 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
176 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
177 <param name="ncol" type="text" value="c1" label="Column if IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
178 <conditional name="foldchange" >
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
179 <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Map quantitative data on the pathway?"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
180 <when value="true">
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
181 <param name="fc_col" type="text" label="Column(s) number of quantitative data (separated by ','. 3 columns max)" help="For example : c1,c3,c4"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
182 </when>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
183 <when value="false"/>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
184 </conditional>
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
185 </when>
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
186 </conditional>
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
187 <!--/section-->
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
188 <param name="native" type="select" label="Graphical format">
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
189 <option value="true">KEGG map (.png)</option>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
190 <option value="false">Graphviz layout engine (.pdf)</option>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
191 </param>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
192 </inputs>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
193 <outputs>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
194 <data name="text_output" format="tsv" label="KEGG maps visualization text output"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
195 <collection type="list" label="KEGG maps visualization from ${input.file.name}" name="graphviz_output_from_file">
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
196 <filter>native=="false" and input["ids"] == "file"</filter>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
197 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.pdf" ext="pdf" />
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
198 </collection>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
199 <collection type="list" label="KEGG maps visualization from ${input.file.name}" name="kegg_graph_output_from_file">
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
200 <filter>native=="true" and input["ids"] == "file"</filter>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
201 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
202 </collection>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
203 <collection type="list" label="KEGG maps visualization" name="graphviz_output_from_list">
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
204 <filter>native=="false" and input["ids"] == "text"</filter>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
205 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.pdf" ext="pdf" />
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
206 </collection>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
207 <collection type="list" label="KEGG maps visualization" name="kegg_graph_output_from_list">
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
208 <filter>native=="true" and input["ids"] == "text"</filter>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
209 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png" />
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
210 </collection>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
211 </outputs>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
212 <tests>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
213 <!--test>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
214 <conditional name="input">
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
215 <param name="ids" value="file"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
216 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
217 <param name="header" value="true"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
218 <param name="ncol" value="c1"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
219 </conditional>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
220 <conditional name="pathways">
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
221 <param name="pathways_id" value="pathways_ids"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
222 <param name="pids" value="04514,05167,00010"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
223 </conditional>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
224 <param name="id_type" value="uniprotID"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
225 <param name="species" value="hsa"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
226 <param name="native" value="true"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
227 <output name="kegg_from_file" file="hsa04514.pathview.png" compare="sim_size"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
228 <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
229 <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
230 </test-->
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
231 </tests>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
232 <help><![CDATA[
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
233
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
234 **Description**
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
235
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
236 This tool based on the Pathview R package, is set for pathway based data integration and visualization.
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
237
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
238 It maps and renders a wide variety of biological data on relevant KEGG pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data.
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
239
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
240 **Input**
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
241
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
242 1. "Enter your pathway(s)": target KEGG Pathways to be specify can be set by:
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
243
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
244 - choosing from the KEGG pathways name list
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
245 - giving a list of KEGG pathway IDs (e.g.hsa00010) (copy/paste mode)
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
246 - selecting a list from a dataset (column) - for instance, output from the "KEGG pathways identification and coverage" tool can be used (1st column, c1)
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
247 2. "Select ID type for genes to map on the pathway(s)": Identifiers to map can be either a list of Entrez genes IDs, KEGG genes ID or Uniprot accession number. IDs to be mapped can be either provided by copy/paste or a file (tabular, tsv, txt) with a column containing the IDs.
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
248 3. "Map quantitative data on the pathway ?": Yes/No (default is No). Fold change values (up to three columns) from a dataset (same file as identifiers to map) can be graphically represented on the final figure (using a range of color representing the fold-change values).
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
249
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
250 Below is an example of an input file with identifiers (uniprot_AC) and fold_change values.
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
251
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
252 .. csv-table:: Simulated data
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
253 :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
254
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
255 "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
256 "P02538","Keratin, type II cytoskeletal 6A","53","-0.988842456122076","0.654626325100182","-0.219153396366064"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
257 "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
258 "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
259
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
260 |
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
261
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
262 .. class:: warningmark
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
263
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
264 If there's more than one ID per line in the specified column, it will be splitted resulting in one unique ID per line. For example this table:
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
265
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
266 .. csv-table:: Simulated data
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
267 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
268
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
269 "ENSG00000136881","Q14032","BAAT_HUMAN"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
270 "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
271 "ENSG00000244731","P0C0L4","CO4A_HUMAN"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
272
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
273 |
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
274
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
275 will be converted as follow:
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
276
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
277 .. csv-table:: Simulated data
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
278 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
279
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
280 "ENSG00000136881","Q14032","BAAT_HUMAN"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
281 "ENSG00000170099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
282 "ENSG00000170099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
283 "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
284 "ENSG00000244731","P0C0L4","CO4A_HUMAN"
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
285
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
286 |
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
287
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
288 -----
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
289
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
290 **Output:**
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
291
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
292 - a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway.
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
293
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
294 - a **summary text file** (.tsv) of the mapping(s) with the following columns
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
295 - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
296 - **pathway name**: name(s) of KEGG pathway(s) used for mapping
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
297 - **nb of Uniprot_AC used** (only when Uniprot accession number is given): number of Uniprot accession number which will be converted to Entrez genes IDs
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
298 - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
299 - **nb of Entrez gene ID mapped**: number of Entrez gene IDs mapped on a given pathway
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
300 - **nb of Entrez gene ID in the pathway**: number total of Entrez gene IDs in a given pathway
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
301 - **ratio of Entrez gene ID mapped**: number of Entrez gene IDs mapped / number total of Entrez gene IDs
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
302 - **Entrez gene ID mapped**: list of mapped Entrez gene IDs
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
303 - **uniprot_AC mapped** (only when Uniprot accession number is given): list of Uniprot accession number corresponding to the mapped Entrez gene IDs
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
304
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
305 -----
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
306
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
307 .. class:: infomark
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
308
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
309 **Data source (release date)**
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
310
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
311 KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
312
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
313 User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
314
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
315 -----
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
316
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
317 .. class:: infomark
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
318
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
319 **Authors**
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
320
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
321 Luo, Weijun, Brouwer, Cory (2013). “Pathview: an R/Bioconductor package for pathway-based data integration and visualization.” Bioinformatics, 29(14), 1830-1831. doi: 10.1093/bioinformatics/btt285.
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
322
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
323 -----
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
324
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
325 .. class:: infomark
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
326
2
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
327 **Galaxy integration**
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
328
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
329 David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
330
8a6863adcd09 planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
proteore
parents: 1
diff changeset
331 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
0
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
332
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
333 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
334
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
335 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
336 ]]></help>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
337 <citations>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
338 <citation type="doi">10.1093/nar/gkx372</citation>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
339 <citation type="bibtex">
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
340 @misc{renameTODO,
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
341 author = {Weijun Luo},
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
342 year = {2013},
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
343 title = {pathview},
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
344 url = {https://bioconductor.org/packages/release/bioc/html/pathview.html},
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
345 }</citation>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
346 </citations>
789acaab8255 planemo upload commit 78ad61e52c2bf8c5ffada89a8eed429a332eb40b-dirty
proteore
parents:
diff changeset
347 </tool>