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author proteore
date Mon, 12 Nov 2018 10:59:49 -0500
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1 <tool id="compute_kegg_pathways" name="KEGG pathways" version="2018.11.12">
2 <description>identification and coverage</description>
3 <requirements>
4 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 Rscript $__tool_directory__/compute_kegg_pathways.R
8
9 #if $input.ids == "text"
10 --id_list="$input.txt"
11 #else
12 --input="$input.file"
13 --id_column="$input.ncol"
14 --header="$input.header"
15 #end if
16
17 --id_type="$id_type"
18 --output="$output1"
19 --nb_pathways="$nb_pathways"
20 --species="$species"
21
22 ]]></command>
23 <inputs>
24 <conditional name="input" >
25 <param name="ids" type="select" label="Enter your identifiers (KEGG genes ID)" help="Copy/paste or ID list from a file (e.g. table)" >
26 <option value="text">Copy/paste your identifiers</option>
27 <option value="file" selected="true">Input file containing your KEGG genes IDs</option>
28 </param>
29 <when value="text" >
30 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by tab,space or carriage return into the form field, for example: hsa:3306 hsa:22948' >
31 <sanitizer invalid_char=''>
32 <valid initial="string.printable">
33 <remove value="&apos;"/>
34 </valid>
35 <mapping initial="none">
36 <add source="&apos;" target="__sq__"/>
37 </mapping>
38 </sanitizer>
39 </param>
40 </when>
41 <when value="file" >
42 <param name="file" type="data" format="txt,tabular,tsv" label="Select a file that contains your list of KEGG gene IDs" help="" />
43 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
44 <param name="ncol" type="text" value="c1" label="The column number of KEGG genes 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' />
45 </when>
46 </conditional>
47 <param name="id_type" type="select" label="select your identifiers type :">
48 <option value="kegg-id">KEGG ID (genes)</option>
49 <!--option value="uniprot">Uniprot Accession number</option-->
50 <option value="ncbi-geneid">Entrez gene ID</option>
51 </param>
52 <param name="species" type="select" label="Select species">
53 <option value="hsa">Human (H. sapiens)</option>
54 <option value="mmu">Mouse (M. musculus)</option>
55 <option value="rno">Rat (R. norvegicus)</option>
56 </param>
57 <param type="integer" name="nb_pathways" label="Set the number of pathways to be displayed in the output" value="10" help="Pathways are sorted by percent of mapping gene by pathway in descending order"/>
58 </inputs>
59 <outputs>
60 <data name="output1" format="tsv" />
61 </outputs>
62 <tests>
63 <test>
64 <conditional name="input" >
65 <param name="ids" value="file"/>
66 <param name="file" value="SPZ.soluble_kegg_id.txt" />
67 <param name="header" value="true" />
68 <param name="ncol" value="c2" />
69 </conditional>
70 <param name="id_type" value="kegg-id" />
71 <param name="species" value="hsa" />
72 <param name="nb_pathways" value="20" />
73 <output name="output1" value="test.tsv" />
74 </test>
75 </tests>
76 <help><![CDATA[
77
78 This tool maps a list of KEGG gene IDs to KEGG pathway and return a list of KEGG pathways ranked by the percentage of coverage for each pathway; this is done by computing the number of KEGG genes IDs from your list divided by the total number of KEGG genes present in the considered species for each KEGG pathway.
79
80 It allows you to directly identify the signaling pathways that are the most covered by your proteomics dataset.
81
82 By default the number of pathway to be displayed is set to 10 and sorted in descending order.
83
84 At the moment three species are supported: Human (Homo sapiens), Mouse (Mus musculus) and Rat (Rattus norvegicus).
85
86 **Input:**
87
88 Input can be either a list of KEGG genes IDs or a file containing multiple columns but with at least one column of KEGG genes IDs (e.g. hsa04970). If your input file contains other type of IDs, please use the ID_Converter tool to get KEGG genes ID.
89
90 **Output:**
91
92 The output is a tabular file (.tsv) with the following columns:
93
94 * **Pathway_ID:** KEGG pathway identifier (e.g. hsa04970)
95 * **Description:** name of the pathway as in KEGG
96 * **Ratio IDs mapped/total IDs (%):** percentage of pathway coverage
97 * **nb KEGG genes IDs mapped in the pathway:** number of KEGG genes of your list mapped on the KEGG pathway
98 * **nb total of KEGG genes IDs present in the pathway:** total number of KEGG genes present in the KEGG pathway
99
100 -----
101
102 .. class:: infomark
103
104 **Database:**
105
106 Pathways and KEGG genes IDs are collected via KEGGREST package.
107
108 User manual / Documentation: KEGGREST Bioconductor package https://bioconductor.org/packages/3.1/bioc/html/KEGGREST.html
109
110
111 -----
112
113 .. class:: infomark
114
115 **Galaxy integration**
116
117 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
118
119 Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
120
121 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
122
123 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
124
125 ]]></help>
126 <citations>
127 <citation type="bibtex">
128 @misc{githubKEGGREST,
129 title = {KEGGREST: Client-side REST access to KEGG},
130 author = {Dan Tenenbaum},
131 year = {2018},
132 note = {R package version 1.18.1},
133 publisher = {GitHub},
134 journal = {GitHub repository},
135 url = {https://github.com/Bioconductor/KEGGREST},
136 }</citation>
137 </citations>
138 </tool>