Mercurial > repos > proteore > proteore_maps_visualization

annotate kegg_maps_visualization.xml @ 4:8e611bdc96ec draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 6bef056b0e52bfa39dbe8591bfe67f8c95bf3ba2-dirty"
author proteore
date Wed, 15 Jan 2020 11:31:03 -0500
parents dfceadc0b703
children 4a3056be0774
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
8e611bdc96ec "planemo upload commit 6bef056b0e52bfa39dbe8591bfe67f8c95bf3ba2-dirty"
proteore
parents: 3
diff changeset
1 <tool id="kegg_maps_visualization" name="Pathways visualization" version="2020.01.08">
2
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
2 <description>of (differentially expressed) genes/proteins [KEGG]</description>
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
3 <requirements>
4
8e611bdc96ec "planemo upload commit 6bef056b0e52bfa39dbe8591bfe67f8c95bf3ba2-dirty"
proteore
parents: 3
diff changeset
4 <requirement type="package" version="3.6.2" >R</requirement>
8e611bdc96ec "planemo upload commit 6bef056b0e52bfa39dbe8591bfe67f8c95bf3ba2-dirty"
proteore
parents: 3
diff changeset
5 <requirement type="package" version="1.26.0">bioconductor-pathview</requirement>
8e611bdc96ec "planemo upload commit 6bef056b0e52bfa39dbe8591bfe67f8c95bf3ba2-dirty"
proteore
parents: 3
diff changeset
6 <requirement type="package" version="1.26.0">bioconductor-keggrest</requirement>
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
7 </requirements>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
9 Rscript $__tool_directory__/kegg_maps_visualization.R
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
10 #if $input.ids == "text"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
11 --id_list="$input.txt"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
12 #else
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
13 --input="$input.file"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
14 --id_column="$input.ncol"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
15 --header="$input.header"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
16 #end if
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
17 #if $species.pathways.pathways_id != "pathways_file"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
18 --pathways_id="$species.pathways.pids"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
19 #else
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
20 --pathways_input="$species.pathways.file"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
21 --header2="$species.pathways.header2"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
22 --pathway_col="$species.pathways.ncol2"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
23 #end if
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
24 --id_type="$id_type"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
25 --native_kegg="$native"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
26
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
27
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
28 #if $input.ids=="file" and $input.foldchange.fc=="true"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
29 --fold_change_data="$input.foldchange.fc"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
30 --fold_change_col="$input.foldchange.fc_col"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
31 #else
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
32 --fold_change_data="false"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
33 #end if
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
34
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
35 --species=${species.ref_file}
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
36 --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] }
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
37 --output="$text_output"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
38
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
39 ]]></command>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
40 <inputs>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
41 <!--section name="pathways_section" title="Pathways" expanded="True"-->
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
42 <conditional name="species">
3
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
43 <param name="ref_file" type="select" label="Species (human, mouse, rat)" >
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
44 <option value="hsa">Human (Homo sapiens)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
45 <option value="mmu">Mouse (Mus musculus)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
46 <option value="rno">Rat (Rattus norvegicus)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
47 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
48 <when value="hsa">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
49 <conditional name="pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
50 <param name="pathways_id" type="select" label="Enter your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
51 <option value="pathways_names">KEGG pathway name(s)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
52 <option value="pathways_ids">KEGG pathway IDs</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
53 <option value="pathways_file">KEGG pathway IDs from file</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
54 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
55 <when value="pathways_names">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
56 <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'>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
57 <options from_data_table="hsa_pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
58 <filter type="sort_by" column="1"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
59 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
60 </options>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
61 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
62 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
63 <when value="pathways_ids">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
64 <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"'>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
65 <sanitizer invalid_char=''>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
66 <valid initial="string.printable">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
67 <remove value="&apos;"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
68 </valid>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
69 <mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
70 <add source="&#x20;" target=""/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
71 </mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
72 </sanitizer>
2
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
73 <validator type="regex" message="Please enter correct pathway id(s)">([a-z]{3}[0-9]{5}[\s]*)+</validator>
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
74 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
75 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
76 <when value="pathways_file">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
77 <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
78 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
2
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
79 <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'>
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
80 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
81 </param>
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
82 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
83 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
84 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
85 <when value="mmu">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
86 <conditional name="pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
87 <param name="pathways_id" type="select" label="Enter your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
88 <option value="pathways_names">KEGG pathway name(s)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
89 <option value="pathways_ids">KEGG pathway IDs</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
90 <option value="pathways_file">KEGG pathway IDs from file</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
91 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
92 <when value="pathways_names">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
93 <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'>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
94 <options from_data_table="mmu_pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
95 <filter type="sort_by" column="1"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
96 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
97 </options>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
98 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
99 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
100 <when value="pathways_ids">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
101 <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"'>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
102 <sanitizer invalid_char=''>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
103 <valid initial="string.printable">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
104 <remove value="&apos;"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
105 </valid>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
106 <mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
107 <add source="&#x20;" target=""/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
108 </mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
109 </sanitizer>
2
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
110 <validator type="regex" message="Please enter correct pathway id(s)">([a-z]{3}[0-9]{5}[\s]*)+</validator>
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
111 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
112 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
113 <when value="pathways_file">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
114 <param name="file" type="data" format="txt,tabular" label="Enter your file" help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
115 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
2
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
116 <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'>
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
117 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
118 </param>
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
119 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
120 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
121 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
122 <when value="rno">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
123 <conditional name="pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
124 <param name="pathways_id" type="select" label="Enter your pathway(s) name/id" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
125 <option value="pathways_names">KEGG pathway name(s)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
126 <option value="pathways_ids">KEGG pathway IDs</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
127 <option value="pathways_file">KEGG pathway IDs from file</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
128 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
129 <when value="pathways_names">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
130 <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'>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
131 <options from_data_table="rno_pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
132 <filter type="sort_by" column="1"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
133 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
134 </options>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
135 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
136 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
137 <when value="pathways_ids">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
138 <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"'>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
139 <sanitizer invalid_char=''>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
140 <valid initial="string.printable">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
141 <remove value="&apos;"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
142 </valid>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
143 <mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
144 <add source="&#x20;" target=""/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
145 </mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
146 </sanitizer>
2
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
147 <validator type="regex" message="Please enter correct pathway id(s)">([a-z]{3}[0-9]{5}[\s]*)+</validator>
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
148 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
149 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
150 <when value="pathways_file">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
151 <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
152 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
2
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
153 <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'>
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
154 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
155 </param>
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
156 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
157 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
158 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
159 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
160 <!--/section-->
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
161 <!--section name="genes_section" title="Genes/prot" expanded="True"-->
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
162 <param name="id_type" type="select" label="Select ID type for genes to map to the pathway(s):">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
163 <option value="geneID" selected="true">Entrez Gene ID</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
164 <option value="keggid">KEGG Genes ID</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
165 <option value="uniprotID">UniProt Accession number</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
166 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
167 <conditional name="input" >
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
168 <param name="ids" type="select" label="Enter your IDs" help="Copy/paste or ID from file (e.g. table)" >
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
169 <option value="text">Copy/paste your IDs</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
170 <option value="file" selected="true">Input file containing your IDs</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
171 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
172 <when value="text" >
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
173 <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' >
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
174 <sanitizer invalid_char=''>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
175 <valid initial="string.printable">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
176 <remove value="&apos;"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
177 </valid>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
178 <mapping initial="none">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
179 <add source="&apos;" target="__sq__"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
180 </mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
181 </sanitizer>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
182 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
183 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
184 <when value="file" >
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
185 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
186 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
2
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
187 <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'>
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
188 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
189 </param>
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
190 <conditional name="foldchange" >
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
191 <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Map quantitative data on the pathway?"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
192 <when value="true">
2
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
193 <param name="fc_col" type="text" label="Column(s) number of quantitative data (separated by ','. 3 columns max)" help="For example : c1,c3,c4">
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
194 <validator type="regex" message="Please enter column numbers, for example: 'c1,c3' for first and third columns">([c]{0,1}[0-9]+[,]*){1,3}</validator>
6ca99419207d planemo upload commit 395d6aa47cce1fb7642b7c06133636c43d80f3c7-dirty
proteore
parents: 1
diff changeset
195 </param>
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
196 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
197 <when value="false"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
198 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
199 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
200 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
201 <!--/section-->
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
202 <param name="native" type="select" label="Graphical format">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
203 <option value="true">KEGG map (.png)</option>
3
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
204 <option value="false">KEGG map, graphviz layout engine (.pdf)</option>
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
205 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
206 </inputs>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
207 <outputs>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
208 <data name="text_output" format="tsv" label="KEGG maps visualization text output"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
209 <collection type="list" label="KEGG maps visualization from ${input.file.name}" name="graphviz_output_from_file">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
210 <filter>native=="false" and input["ids"] == "file"</filter>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
211 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.pdf" ext="pdf" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
212 </collection>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
213 <collection type="list" label="KEGG maps visualization from ${input.file.name}" name="kegg_graph_output_from_file">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
214 <filter>native=="true" and input["ids"] == "file"</filter>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
215 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
216 </collection>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
217 <collection type="list" label="KEGG maps visualization" name="graphviz_output_from_list">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
218 <filter>native=="false" and input["ids"] == "text"</filter>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
219 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.pdf" ext="pdf" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
220 </collection>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
221 <collection type="list" label="KEGG maps visualization" name="kegg_graph_output_from_list">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
222 <filter>native=="true" and input["ids"] == "text"</filter>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
223 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
224 </collection>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
225 </outputs>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
226 <tests>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
227 <!--test>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
228 <conditional name="input">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
229 <param name="ids" value="file"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
230 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
231 <param name="header" value="true"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
232 <param name="ncol" value="c1"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
233 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
234 <conditional name="pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
235 <param name="pathways_id" value="pathways_ids"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
236 <param name="pids" value="04514,05167,00010"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
237 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
238 <param name="id_type" value="uniprotID"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
239 <param name="species" value="hsa"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
240 <param name="native" value="true"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
241 <output name="kegg_from_file" file="hsa04514.pathview.png" compare="sim_size"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
242 <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
243 <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
244 </test-->
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
245 </tests>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
246 <help><![CDATA[
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
247
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
248 **Description**
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
249
3
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
250 This tool, relying on the Pathview R package, is set for pathway based data integration and visualization.
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
251
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
252 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.
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
253
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
254 **Input**
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
255
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
256 1. "Enter your pathway(s)": target KEGG Pathways to be specify can be set by:
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
257
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
258 - choosing from the KEGG pathways name list
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
259 - giving a list of KEGG pathway IDs (e.g.hsa00010) (copy/paste mode)
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
260 - selecting a list from a dataset (column) - for instance, output from the "KEGG pathways identification and coverage" tool can be used (1st column, c1)
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
261 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.
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
262 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).
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
263
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
264 Below is an example of an input file with identifiers (uniprot_AC) and fold_change values.
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
265
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
266 .. csv-table:: Simulated data
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
267 :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
268
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
269 "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
270 "P02538","Keratin, type II cytoskeletal 6A","53","-0.988842456122076","0.654626325100182","-0.219153396366064"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
271 "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
272 "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
273
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
274 |
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
275
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
276 .. class:: warningmark
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
277
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
278 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:
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
279
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
280 .. csv-table:: Simulated data
3
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
281 :header: "Entrez_gene_ID","UniProt.AC","UniProt.ID"
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
282
3
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
283 "6881","Q14032","BAAT_HUMAN"
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
284 "70099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
285 "731","P0C0L4","CO4A_HUMAN"
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
286
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
287 |
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
288
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
289 will be converted as follow:
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
290
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
291 .. csv-table:: Simulated data
3
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
292 :header: "Entrez_gene_ID","UniProt.AC","UniProt.ID"
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
293
3
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
294 "6881","Q14032","BAAT_HUMAN"
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
295 "70099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
296 "70099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
297 "70099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
298 "731","P0C0L4","CO4A_HUMAN"
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
299
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
300 |
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
301
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
302 -----
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
303
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
304 **Output:**
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
305
3
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
306 - a set of graphical map, i.e. a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each KEGG map.
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
307
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
308 - a **summary text file** (.tsv) of the mapping(s) with the following columns
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
309 - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
310 - **pathway name**: name(s) of KEGG pathway(s) used for mapping
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
311 - **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
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
312 - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
313 - **nb of Entrez gene ID mapped**: number of Entrez gene IDs mapped on a given pathway
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
314 - **nb of Entrez gene ID in the pathway**: number total of Entrez gene IDs in a given pathway
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
315 - **ratio of Entrez gene ID mapped**: number of Entrez gene IDs mapped / number total of Entrez gene IDs
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
316 - **Entrez gene ID mapped**: list of mapped Entrez gene IDs
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
317 - **uniprot_AC mapped** (only when Uniprot accession number is given): list of Uniprot accession number corresponding to the mapped Entrez gene IDs
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
318
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
319 -----
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
320
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
321 .. class:: infomark
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
322
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
323 **Data source (release date)**
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
324
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
325 KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
326
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
327 User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
328
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
329 -----
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
330
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
331 .. class:: infomark
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
332
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
333 **Authors**
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
334
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
335 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.
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
336
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
337 -----
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
338
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
339 .. class:: infomark
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
340
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
341 **Galaxy integration**
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
342
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
343 David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
344
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
345 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
346
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
347 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
348
3
dfceadc0b703 planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
proteore
parents: 2
diff changeset
349 Help: contact@proteore.org for any questions or concerns about this tool.
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
350 ]]></help>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
351 <citations>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
352 <citation type="doi">10.1093/nar/gkx372</citation>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
353 <citation type="bibtex">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
354 @misc{renameTODO,
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
355 author = {Weijun Luo},
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
356 year = {2013},
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
357 title = {pathview},
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
358 url = {https://bioconductor.org/packages/release/bioc/html/pathview.html},
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
359 }</citation>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
360 </citations>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
361 </tool>