Mercurial > repos > proteore > proteore_protein_interaction_maps

annotate build_protein_interaction_maps.xml @ 1:07222528456f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Deleted selected files
author proteore
date Fri, 01 Mar 2019 12:03:25 -0500
parents 3fcdc585cd2e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
1 <tool id="build_protein_interaction_maps" name="Build protein interaction maps" version="2019.03.01">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
2 <requirements>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
3 </requirements>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
4 <command detect_errors="exit_code"><![CDATA[
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
5 python $__tool_directory__/build_protein_interaction_maps.py
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
6 #if $input.ids == "text"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
7 --input="$input.txt"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
8 --input_type="text"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
9 #else
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
10 --input="$input.file"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
11 --ncol="$input.ncol"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
12 --header="$input.header"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
13 --input_type="file"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
14 #end if
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
15 --database=$database.ref
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
16 #if $database.ref=="biogrid"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
17 --species="${ filter( lambda x: str( x[3] ) == str( $database.ref_file ), $__app__.tool_data_tables['proteore_biogrid_dictionaries'].get_fields() )[0][2] }"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
18 #else
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
19 --species="Human"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
20 #end if
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
21
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
22 #if 'PPI_dictionaries' in str($database.ref_file).split('/') :
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
23 --dict_path="$database.ref_file"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
24 #else
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
25 --dict_path="$__tool_data_path__/$database.ref_file"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
26 #end if
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
27
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
28 #if $input.ids == "file"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
29 --network_output="$network_output"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
30 --nodes_output="$nodes_output"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
31 #else
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
32 --network_output="$network_output_from_list"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
33 --nodes_output="$nodes_output_from_list"
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
34 #end if
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
35 --id_type=$database.id_type
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
36
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
37 ]]></command>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
38 <inputs>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
39 <conditional name="input">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
40 <param name="ids" type="select" label="Enter IDs" help="Copy/paste or from a file (e.g. table)">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
41 <option value="text">Copy/paste your identifiers</option>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
42 <option value="file" selected="true">Input file containing IDs</option>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
43 </param>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
44 <when value="text">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
45 <param name="txt" type="text" label="Copy/paste IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: P31946 P62258' >
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
46 <sanitizer invalid_char="">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
47 <valid initial="string.printable">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
48 <remove value="&apos;"/>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
49 </valid>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
50 <mapping initial="none">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
51 <add source="&apos;" target="__sq__"/>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
52 <add source="&#x20;" target=""/>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
53 <add source="&#xA;" target=""/>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
54 <add source="&#xD;" target=""/>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
55 <add source="&#x9;" target=""/>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
56 </mapping>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
57 </sanitizer>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
58 </param>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
59 </when>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
60 <when value="file" >
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
61 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
62 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
63 <param name="ncol" type="text" value="c1" label="Column number of 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'>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
64 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
65 </param>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
66 </when>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
67 </conditional>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
68 <conditional name="database">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
69 <param name="ref" type="select" label="Select database">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
70 <option value="biogrid">BioGRID</option>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
71 <option value="bioplex">Human Bioplex 2.0</option>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
72 <option value="humap">Human protein complex Map (Hu.map)</option>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
73 </param>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
74 <when value="biogrid">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
75 <param name="id_type" type="select" label="Type/source of IDs" optional="false" >
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
76 <option value="GeneID" >Entrez gene ID</option>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
77 </param>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
78 <param name="ref_file" type="select" label="Species">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
79 <options from_data_table="proteore_biogrid_dictionaries" />
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
80 </param>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
81 </when>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
82 <when value="bioplex">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
83 <param name="id_type" type="select" label="Type/source of IDs" optional="false">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
84 <option value="UniProt-AC" selected="True" >UniProt accession number</option>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
85 <option value="GeneID">Entrez gene ID</option>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
86 </param>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
87 <param name="ref_file" type="select" label="Species">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
88 <options from_data_table="proteore_bioplex_dictionaries" />
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
89 </param>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
90 </when>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
91 <when value="humap">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
92 <param name="id_type" type="select" label="Type/source of IDs" optional="false" >
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
93 <option value="GeneID" >Entrez gene ID</option>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
94 </param>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
95 <param name="ref_file" type="select" label="Species">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
96 <options from_data_table="proteore_humap_dictionaries" />
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
97 </param>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
98 </when>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
99 </conditional>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
100 </inputs>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
101 <outputs>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
102 <data name="network_output_from_list" format="tsv" label="Network_${database.ref}_from_ids_list">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
103 <filter>input['ids'] == "text" </filter>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
104 </data>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
105 <data name="network_output" format="tsv" label="Network_${database.ref}_from_${input.file.name}">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
106 <filter>input['ids'] == "file" </filter>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
107 </data>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
108 <data name="nodes_output_from_list" format="tsv" label="Nodes_${database.ref}_from_ids_list">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
109 <filter>input['ids'] == "text"</filter>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
110 </data>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
111 <data name="nodes_output" format="tsv" label="Nodes_${database.ref}_from_${input.file.name}">
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
112 <filter>input['ids'] == "file"</filter>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
113 </data>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
114 </outputs>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
115 <help><![CDATA[
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
116 **Description**
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
117
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
118 -----
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
119
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
120 **Input**
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
121
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
122 Id list of Entrez gene ID or Uniprot-AC from copy/paste or file
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
123
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
124 -----
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
125
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
126 **Parameters**
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
127
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
128 - **biogrid**
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
129 - **bioplex**
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
130 - **hu.map**
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
131
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
132 -----
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
133
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
134 **Output**
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
135
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
136 - **network_file**
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
137 - **nodes_file**
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
138
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
139 -----
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
140
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
141 **Data sources (release date)**
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
142
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
143 This tool uses the following interactomes:
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
144
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
145 **biogrid**
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
146
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
147 - BIOGRID-ORGANISM-Homo_sapiens-3.5.167.tab2.txt
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
148 - BIOGRID-ORGANISM-Mus_musculus-3.5.167.tab2.txt
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
149 - BIOGRID-ORGANISM-Rattus_norvegicus-3.5.167.tab2.txt
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
150 - NCBI2Reactome.txt: 'https://www.reactome.org/download/current/NCBI2Reactome.txt'
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
151
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
152 from https://downloads.thebiogrid.org/BioGRID/Release-Archive/BIOGRID-3.5.167/
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
153
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
154 **bioplex**
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
155
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
156 - BioPlex_interactionList_v4a.tsv: http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
157 - UniProt2Reactome.txt: https://downloads.thebiogrid.org/BioGRID/Release-Archive/BIOGRID-3.5.167/
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
158 - NCBI2Reactome.txt: 'https://www.reactome.org/download/current/NCBI2Reactome.txt'
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
159
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
160 **Human protein complex Map (Hu.map)
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
161
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
162 - nodeTable.txt: http://proteincomplexes.org/static/downloads/nodeTable.txt
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
163 - pairsWprob: http://proteincomplexes.org/static/downloads/pairsWprob.txt
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
164 - NCBI2Reactome.txt: 'https://www.reactome.org/download/current/NCBI2Reactome.txt'
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
165
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
166 -----
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
167
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
168 .. class:: infomark
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
169
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
170 **Authors**
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
171
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
172 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
173
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
174 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
175
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
176 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
177
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
178 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
179 ]]></help>
3fcdc585cd2e planemo upload commit 696e05eadff826a980b1150be5db5d1f52d06b1b-dirty
proteore
parents:
diff changeset
180 </tool>