Mercurial > repos > proteore > proteore_compute_kegg_pathways

annotate compute_kegg_pathways.xml @ 4:7d8848c4dbb7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 229c140e131039467e2797f656d9acf916907dd7-dirty
author proteore
date Tue, 18 Sep 2018 09:54:58 -0400
parents 0d5c21cc29f7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
7d8848c4dbb7 planemo upload commit 229c140e131039467e2797f656d9acf916907dd7-dirty
proteore
parents: 3
diff changeset
1 <tool id="compute_kegg_pathways" name="KEGG pathways coverage" version="2018.09.18">
0
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
2 <requirements>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
3 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
4 </requirements>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
5 <command detect_errors="exit_code"><![CDATA[
1
1704d57a04ba planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents: 0
diff changeset
6 Rscript $__tool_directory__/compute_kegg_pathways.R
0
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
7
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
8 #if $input.ids == "text"
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
9 --id_list="$input.txt"
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
10 #else
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
11 --input="$input.file"
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
12 --id_column="$input.ncol"
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
13 --header="$input.header"
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
14 #end if
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
15
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
16 --id_type="$ref_ids.id_type"
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
17 --output="$output1"
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
18 --nb_pathways="$nb_pathways"
2
39d3478fbc5e planemo upload commit eed8cd910cd0eb3992d2188485b6ac5fdbc55eea
proteore
parents: 1
diff changeset
19 --ref="$__tool_directory__/$ref_ids.ref_file"
0
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
20
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
21 ]]></command>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
22 <inputs>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
23 <conditional name="input" >
2
39d3478fbc5e planemo upload commit eed8cd910cd0eb3992d2188485b6ac5fdbc55eea
proteore
parents: 1
diff changeset
24 <param name="ids" type="select" label="Provide your identifiers (Uniprot or Entrez gene)" help="Copy/paste or ID list from a file (e.g. table)" >
0
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
25 <option value="text">Copy/paste your identifiers</option>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
26 <option value="file" selected="true">Input file containing your identifiers</option>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
27 </param>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
28 <when value="text" >
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
29 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," into the form field, for example: P31946,P62258' >
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
30 <sanitizer invalid_char=''>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
31 <valid initial="string.printable">
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
32 <remove value="&apos;"/>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
33 </valid>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
34 <mapping initial="none">
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
35 <add source="&apos;" target="__sq__"/>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
36 </mapping>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
37 </sanitizer>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
38 </param>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
39 </when>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
40 <when value="file" >
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
41 <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" />
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
42 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
43 <param name="ncol" type="text" value="c1" label="The 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' />
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
44 </when>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
45 </conditional>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
46 <conditional name="ref_ids">
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
47 <param name="id_type" type="select" label="select your identifiers type :">
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
48 <option value="uniprot">Uniprot Accession number</option>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
49 <option value="geneID">Entrez gene ID</option>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
50 </param>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
51 <when value="uniprot">
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
52 <param name="ref_file" type="select" label="Select species" >
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
53 <options from_data_table="uniprot_kegg_list"/>
2
39d3478fbc5e planemo upload commit eed8cd910cd0eb3992d2188485b6ac5fdbc55eea
proteore
parents: 1
diff changeset
54 <option>Human (Homo sapiens)</option>
39d3478fbc5e planemo upload commit eed8cd910cd0eb3992d2188485b6ac5fdbc55eea
proteore
parents: 1
diff changeset
55 <option>Mouse (Mus musculus)</option>
0
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
56 </param>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
57 </when>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
58 <when value="geneID">
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
59 <param name="ref_file" type="select" label="Select species" >
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
60 <options from_data_table="entrez_kegg_list"/>
2
39d3478fbc5e planemo upload commit eed8cd910cd0eb3992d2188485b6ac5fdbc55eea
proteore
parents: 1
diff changeset
61 <option>Human (Homo sapiens)</option>
39d3478fbc5e planemo upload commit eed8cd910cd0eb3992d2188485b6ac5fdbc55eea
proteore
parents: 1
diff changeset
62 <option>Mouse (Mus musculus)</option>
0
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
63 </param>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
64 </when>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
65 </conditional>
2
39d3478fbc5e planemo upload commit eed8cd910cd0eb3992d2188485b6ac5fdbc55eea
proteore
parents: 1
diff changeset
66 <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"/>
0
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
67 </inputs>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
68 <outputs>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
69 <data name="output1" format="tsv" />
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
70 </outputs>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
71 <help><![CDATA[
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
72
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
73 This tool computes the number of proteins from your list divided by the total number of protein of each KEGG pathway.
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
74
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
75 it allows you to identify the signaling pathways that are the most covered by your proteomics dataset.
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
76
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
77 By default the number of pathway to be displayed is set to 10 and sorted in descending order.
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
78
2
39d3478fbc5e planemo upload commit eed8cd910cd0eb3992d2188485b6ac5fdbc55eea
proteore
parents: 1
diff changeset
79 At the moment two species are supported: Human (Homo sapiens) and Mouse (Mus musculus)
0
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
80
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
81 **Input:**
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
82
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
83 Input can be either a list of Uniprot accession number or Entrez gene IDs (copy/paste mode) or a file containing multiple columns but with at least one column Uniprot accession number or Entrez gene IDs. If your input file contains other type of IDs, please use the ID_Converter tool.
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
84
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
85 **Output:**
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
86
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
87 The output is a tabular file (.tsv) with the following columns:
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
88
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
89 * **Pathway_ID:** KEGG pathway identifier (e.g. hsa04970)
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
90 * **Description:** name of the pathway as in KEGG
3
0d5c21cc29f7 planemo upload commit 0be58bb700f64de6792a7234a11675bae2755e8f-dirty
proteore
parents: 2
diff changeset
91 * **Ratio IDs mapped/total IDs (%):** percentage of pathway coverage
0d5c21cc29f7 planemo upload commit 0be58bb700f64de6792a7234a11675bae2755e8f-dirty
proteore
parents: 2
diff changeset
92 * **nb genes mapped in the pathway:** number of genes/proteins of your list mapped on the KEGG pathway
0d5c21cc29f7 planemo upload commit 0be58bb700f64de6792a7234a11675bae2755e8f-dirty
proteore
parents: 2
diff changeset
93 * **nb total genes present in the pathway:** total number of genes/proteins present in the KEGG pathway
0
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
94
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
95 -----
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
96
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
97 .. class:: infomark
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
98
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
99 **Database:**
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
100
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
101 Pathways and associated Uniprot Accession Number or Gene IDs are collected from KEGGREST package
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
102
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
103 User manual / Documentation: KEGGREST Bioconductor package https://bioconductor.org/packages/3.1/bioc/html/KEGGREST.html
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
104
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
105
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
106 -----
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
107
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
108 .. class:: infomark
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
109
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
110 **Galaxy integration**
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
111
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
112 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
113
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
114 Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
115
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
116 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
117
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
118 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
119
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
120 -----
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
121
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
122 compute_KEGG_pathways R script
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
123
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
124 | Arguments:
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
125 | --**help** Print this test
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
126 | --**input** tab file
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
127 | --**id_list** id list ',' separated
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
128 | --**id_type** type of input ids (uniprot_AC or geneID)
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
129 | --**id_column** number og column containg ids of interest
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
130 | --**org** organism : Hs , Mm, ...
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
131 | --**nb_pathways** number of pathways to return
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
132 | --**header** boolean
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
133 | --**output** output path
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
134 | --**ref** ref file (l.hsa.gene.RData, l.hsa.up.RData)
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
135 |
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
136 | Example:
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
137 | Rscript compute_KEGG_pathways.R --input='P31946,P62258' --id_type='uniprot' --id_column 'c1' --header TRUE
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
138 |
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
139
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
140 ]]></help>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
141 <citations>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
142 <citation type="bibtex">
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
143 @misc{githubKEGGREST,
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
144 title = {KEGGREST: Client-side REST access to KEGG},
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
145 author = {Dan Tenenbaum},
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
146 year = {2018},
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
147 note = {R package version 1.18.1},
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
148 publisher = {GitHub},
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
149 journal = {GitHub repository},
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
150 url = {https://github.com/Bioconductor/KEGGREST},
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
151 }</citation>
0fe3cb50fbf6 planemo upload commit 5ba22c155f8fa4a858eea9a23926c739b4722bb3-dirty
proteore
parents:
diff changeset
152 </citations>
2
39d3478fbc5e planemo upload commit eed8cd910cd0eb3992d2188485b6ac5fdbc55eea
proteore
parents: 1
diff changeset
153 </tool>