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comparison kegg_identification.xml @ 3:e7b3609160c5 draft

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planemo upload commit 6854718828a7478905b41fb92d6f96ab41896e84-dirty
author proteore
date Tue, 14 May 2019 08:51:46 -0400
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1 <tool id="kegg_identification" name="Pathways identification" version="2019.05.14">
2 <description>and coverage [KEGG]</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__/kegg_identification.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 IDs (Entrez gene IDs, KEGG gene IDs or UniProt Accession number)" help="Copy/paste or from a file (e.g. table)" >
26 <option value="text">Copy/paste your IDs</option>
27 <option value="file" selected="true">Input file containing your IDs</option>
28 </param>
29 <when value="text" >
30 <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: 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 your file" help="" />
43 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
44 <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
45 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
46 </param>
47 </when>
48 </conditional>
49 <param name="id_type" type="select" label="Select IDs" >
50 <option value="ncbi-geneid" selected="true">Entrez Gene ID</option>
51 <option value="kegg-id">KEGG gene ID</option>
52 <option value="uniprot">UniProt Accession number</option>
53
54 </param>
55 <param name="species" type="select" label="Species">
56 <option value="hsa">Human (Homo sapiens)</option>
57 <option value="mmu">Mouse (Mus musculus)</option>
58 <option value="rno">Rat (Rattus norvegicus)</option>
59 </param>
60 <param type="integer" name="nb_pathways" label="Set number of pathways to be displayed" value="10" help="Pathways are sorted by percent of mapping gene by pathway in descending order"/>
61 </inputs>
62 <outputs>
63 <data name="output1" format="tsv" />
64 </outputs>
65 <tests>
66 <test>
67 <conditional name="input" >
68 <param name="ids" value="file"/>
69 <param name="file" value="SPZ.soluble_kegg_id.txt" />
70 <param name="header" value="true" />
71 <param name="ncol" value="c2" />
72 </conditional>
73 <param name="id_type" value="kegg-id" />
74 <param name="species" value="hsa" />
75 <param name="nb_pathways" value="20" />
76 <output name="output1" value="test.tsv" />
77 </test>
78 </tests>
79 <help><![CDATA[
80
81 **Description**
82
83 This tool maps a list of identifiers to all KEGG pathways and returns a list of KEGG pathways sorted 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 ID of the selected species for each KEGG pathway.
84
85 It allows you to directly identify KEGG pathways that are the most covered by your gene/protein list.
86
87 -----
88
89 **Input**
90
91 Input can be either a list of IDs or a file containing multiple columns but with at least one column of IDs (e.g. hsa:04970).
92 Input IDs type can be Entrez gene ID (e.g. 2243), KEGG gene ID (e.g. hsa:2243 in homo sapiens) or Uniprot accession number (e.g. P02671).
93
94 .. class:: warningmark
95
96 If you use Uniprot accession number, it will be converted to KEGG gene ID; this step can be time consuming.
97
98 If your input file contains other type of ID, please use the ID_Converter tool.
99
100 -----
101
102 **Parameters**
103
104 "Set number of pathways to be displayed": by default the number of pathway to be displayed is set to 10 and sorted in descending order.
105
106 "Species": three species are supported: Human (Homo sapiens), Mouse (Mus musculus) and Rat (Rattus norvegicus).
107
108 -----
109
110 **Output:**
111
112 The output is a tabular file (.tsv) with the following columns:
113
114 * **Pathway_ID:** KEGG pathway identifier (e.g. hsa04970)
115 * **Description:** name of the pathway as in KEGG
116 * **Ratio IDs mapped/total IDs (%):** pathway coverage in percentage
117 * **nb KEGG genes IDs mapped in the pathway:** number of KEGG genes from your list mapped to the KEGG pathway
118 * **nb total of KEGG genes IDs present in the pathway:** total number of KEGG genes present in the KEGG pathway
119
120 -----
121
122 .. class:: infomark
123
124 **Data source (release date)**
125
126 Pathways and KEGG genes IDs are collected via KEGGREST package.
127
128 User manual / Documentation: KEGGREST Bioconductor package https://bioconductor.org/packages/3.1/bioc/html/KEGGREST.html
129
130 -----
131
132 .. class:: infomark
133
134 **Galaxy integration**
135
136 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
137
138 Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
139
140 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
141
142 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
143
144 ]]></help>
145 <citations>
146 <citation type="bibtex">
147 @misc{githubKEGGREST,
148 title = {KEGGREST: Client-side REST access to KEGG},
149 author = {Dan Tenenbaum},
150 year = {2018},
151 note = {R package version 1.18.1},
152 publisher = {GitHub},
153 journal = {GitHub repository},
154 url = {https://github.com/Bioconductor/KEGGREST},
155 }</citation>
156 </citations>
157 </tool>