annotate kegg_maps_visualization.xml @ 0:9845dc9c7323 draft

planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
author proteore
date Tue, 18 Dec 2018 10:02:54 -0500
parents
children 6f389729a30b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
1 <tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2018.12.18">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
2 <description>of (differentially expressed) genes/proteins</description>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
3 <requirements>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
4 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
5 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
6 </requirements>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
8 Rscript $__tool_directory__/kegg_maps_visualization.R
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
9 #if $input.ids == "text"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
10 --id_list="$input.txt"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
11 #else
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
12 --input="$input.file"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
13 --id_column="$input.ncol"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
14 --header="$input.header"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
15 #end if
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
16 #if $species.pathways.pathways_id != "pathways_file"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
17 --pathways_id="$species.pathways.pids"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
18 #else
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
19 --pathways_input="$species.pathways.file"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
20 --header2="$species.pathways.header2"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
21 --pathway_col="$species.pathways.ncol2"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
22 #end if
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
23 --id_type="$id_type"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
24 --native_kegg="$native"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
25
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
26
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
27 #if $input.ids=="file" and $input.foldchange.fc=="true"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
28 --fold_change_data="$input.foldchange.fc"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
29 --fold_change_col="$input.foldchange.fc_col"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
30 #else
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
31 --fold_change_data="false"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
32 #end if
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
33
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
34 --species=${species.ref_file}
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
35 --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] }
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
36 --output="$text_output"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
37
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
38 ]]></command>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
39 <inputs>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
40 <!--section name="pathways_section" title="Pathways" expanded="True"-->
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
41 <conditional name="species">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
42 <param name="ref_file" type="select" label="Species" >
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
43 <option value="hsa">Human (Homo sapiens)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
44 <option value="mmu">Mouse (Mus musculus)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
45 <option value="rno">Rat (Rattus norvegicus)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
46 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
47 <when value="hsa">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
48 <conditional name="pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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)">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
50 <option value="pathways_names">KEGG pathway name(s)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
51 <option value="pathways_ids">KEGG pathway IDs</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
52 <option value="pathways_file">KEGG pathway IDs from file</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
53 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
54 <when value="pathways_names">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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'>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
56 <options from_data_table="hsa_pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
57 <filter type="sort_by" column="1"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
58 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
59 </options>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
60 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
61 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
62 <when value="pathways_ids">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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"'>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
64 <sanitizer invalid_char=''>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
65 <valid initial="string.printable">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
66 <remove value="&apos;"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
67 </valid>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
68 <mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
69 <add source="&#x20;" target=""/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
70 </mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
71 </sanitizer>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
72 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
73 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
74 <when value="pathways_file">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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'" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
76 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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' />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
78 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
79 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
80 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
81 <when value="mmu">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
82 <conditional name="pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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)">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
84 <option value="pathways_names">KEGG pathway name(s)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
85 <option value="pathways_ids">KEGG pathway IDs</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
86 <option value="pathways_file">KEGG pathway IDs from file</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
87 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
88 <when value="pathways_names">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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'>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
90 <options from_data_table="mmu_pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
91 <filter type="sort_by" column="1"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
92 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
93 </options>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
94 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
95 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
96 <when value="pathways_ids">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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"'>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
98 <sanitizer invalid_char=''>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
99 <valid initial="string.printable">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
100 <remove value="&apos;"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
101 </valid>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
102 <mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
103 <add source="&#x20;" target=""/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
104 </mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
105 </sanitizer>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
106 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
107 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
108 <when value="pathways_file">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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'" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
110 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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' />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
112 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
113 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
114 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
115 <when value="rno">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
116 <conditional name="pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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)">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
118 <option value="pathways_names">KEGG pathway name(s)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
119 <option value="pathways_ids">KEGG pathway IDs</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
120 <option value="pathways_file">KEGG pathway IDs from file</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
121 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
122 <when value="pathways_names">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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'>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
124 <options from_data_table="rno_pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
125 <filter type="sort_by" column="1"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
126 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
127 </options>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
128 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
129 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
130 <when value="pathways_ids">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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"'>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
132 <sanitizer invalid_char=''>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
133 <valid initial="string.printable">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
134 <remove value="&apos;"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
135 </valid>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
136 <mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
137 <add source="&#x20;" target=""/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
138 </mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
139 </sanitizer>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
140 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
141 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
142 <when value="pathways_file">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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'" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
144 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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' />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
146 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
147 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
148 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
149 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
150 <!--/section-->
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
151 <!--section name="genes_section" title="Genes/prot" expanded="True"-->
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
152 <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
153 <option value="geneID" selected="true">Entrez Gene ID</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
154 <option value="keggid">KEGG Genes ID</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
155 <option value="uniprotID">UniProt Accession number</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
156 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
157 <conditional name="input" >
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
158 <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
159 <option value="text">Copy/paste your IDs</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
160 <option value="file" selected="true">Input file containing your IDs</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
161 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
162 <when value="text" >
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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' >
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
164 <sanitizer invalid_char=''>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
165 <valid initial="string.printable">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
166 <remove value="&apos;"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
167 </valid>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
168 <mapping initial="none">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
169 <add source="&apos;" target="__sq__"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
170 </mapping>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
171 </sanitizer>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
172 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
173 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
174 <when value="file" >
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
175 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
176 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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' />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
178 <conditional name="foldchange" >
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
179 <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
180 <when value="true">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
182 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
183 <when value="false"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
184 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
185 </when>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
186 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
187 <!--/section-->
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
188 <param name="native" type="select" label="Graphical format">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
189 <option value="true">KEGG map (.png)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
190 <option value="false">Graphviz layout engine (.pdf)</option>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
191 </param>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
192 </inputs>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
193 <outputs>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
194 <data name="text_output" format="tsv" label="KEGG maps visualization text output"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
195 <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
196 <filter>native=="false" and input["ids"] == "file"</filter>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
197 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.pdf" ext="pdf" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
198 </collection>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
199 <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
200 <filter>native=="true" and input["ids"] == "file"</filter>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
201 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
202 </collection>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
203 <collection type="list" label="KEGG maps visualization" name="graphviz_output_from_list">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
204 <filter>native=="false" and input["ids"] == "text"</filter>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
205 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.pdf" ext="pdf" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
206 </collection>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
207 <collection type="list" label="KEGG maps visualization" name="kegg_graph_output_from_list">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
208 <filter>native=="true" and input["ids"] == "text"</filter>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
209 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png" />
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
210 </collection>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
211 </outputs>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
212 <tests>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
213 <!--test>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
214 <conditional name="input">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
215 <param name="ids" value="file"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
216 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
217 <param name="header" value="true"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
218 <param name="ncol" value="c1"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
219 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
220 <conditional name="pathways">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
221 <param name="pathways_id" value="pathways_ids"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
222 <param name="pids" value="04514,05167,00010"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
223 </conditional>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
224 <param name="id_type" value="uniprotID"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
225 <param name="species" value="hsa"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
226 <param name="native" value="true"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
227 <output name="kegg_from_file" file="hsa04514.pathview.png" compare="sim_size"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
228 <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
229 <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
230 </test-->
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
231 </tests>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
232 <help><![CDATA[
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
233
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
234 **Description**
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
235
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
236 This tool based on the Pathview R package, is set for pathway based data integration and visualization.
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
237
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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.
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
239
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
240 **Input**
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
241
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
242 1. "Enter your pathway(s)": target KEGG Pathways to be specify can be set by:
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
243
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
244 - choosing from the KEGG pathways name list
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
245 - giving a list of KEGG pathway IDs (e.g.hsa00010) (copy/paste mode)
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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)
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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.
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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).
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
249
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
250 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
251
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
252 .. csv-table:: Simulated data
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
253 :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
254
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
255 "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
256 "P02538","Keratin, type II cytoskeletal 6A","53","-0.988842456122076","0.654626325100182","-0.219153396366064"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
257 "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
258 "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
259
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
260 |
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
261
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
262 .. class:: warningmark
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
263
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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:
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: "Ensembl_Gene","UniProt.AC","UniProt.ID"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
268
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
269 "ENSG00000136881","Q14032","BAAT_HUMAN"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
270 "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
271 "ENSG00000244731","P0C0L4","CO4A_HUMAN"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
272
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 will be converted as follow:
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
276
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
277 .. csv-table:: Simulated data
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
278 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
279
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
280 "ENSG00000136881","Q14032","BAAT_HUMAN"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
281 "ENSG00000170099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
282 "ENSG00000170099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
283 "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
284 "ENSG00000244731","P0C0L4","CO4A_HUMAN"
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
285
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
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
290 **Output:**
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
291
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
292 - a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway.
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
293
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
294 - a **summary text file** (.tsv) of the mapping(s) with the following columns
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
295 - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
296 - **pathway name**: name(s) of KEGG pathway(s) used for mapping
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
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
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
298 - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
299 - **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
300 - **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
301 - **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
302 - **Entrez gene ID mapped**: list of mapped Entrez gene IDs
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
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
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
304
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
305 -----
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
306
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
307 .. class:: infomark
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
308
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
309 **Data source (release date)**
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
310
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
311 KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
312
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
313 User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
314
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
315 -----
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
316
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
317 .. class:: infomark
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
318
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
319 **Authors**
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
320
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
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.
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
322
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
323 -----
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
324
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
325 .. class:: infomark
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
326
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
327 **Galaxy integration**
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
328
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
329 David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
330
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
331 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
332
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
333 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
334
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
335 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
336 ]]></help>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
337 <citations>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
338 <citation type="doi">10.1093/nar/gkx372</citation>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
339 <citation type="bibtex">
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
340 @misc{renameTODO,
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
341 author = {Weijun Luo},
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
342 year = {2013},
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
343 title = {pathview},
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
344 url = {https://bioconductor.org/packages/release/bioc/html/pathview.html},
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
345 }</citation>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
346 </citations>
9845dc9c7323 planemo upload commit ad5f1c5a1a71d7fa2bc8bac408856aa80b0fc2a3
proteore
parents:
diff changeset
347 </tool>