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comparison kegg_identification.xml @ 2:ae9c1f1cdec3 draft default tip

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planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
author proteore
date Tue, 18 Dec 2018 09:22:24 -0500
parents def6441d2345
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1:def6441d2345 2:ae9c1f1cdec3
20 --species="$species" 20 --species="$species"
21 21
22 ]]></command> 22 ]]></command>
23 <inputs> 23 <inputs>
24 <conditional name="input" > 24 <conditional name="input" >
25 <param name="ids" type="select" label="Enter your list of identifiers" help="Copy/paste or ID list from a file (e.g. table)" > 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 identifiers</option> 26 <option value="text">Copy/paste your IDs</option>
27 <option value="file" selected="true">Input file containing your identifiers</option> 27 <option value="file" selected="true">Input file containing your IDs</option>
28 </param> 28 </param>
29 <when value="text" > 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' > 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=''> 31 <sanitizer invalid_char=''>
32 <valid initial="string.printable"> 32 <valid initial="string.printable">
33 <remove value="&apos;"/> 33 <remove value="&apos;"/>
34 </valid> 34 </valid>
35 <mapping initial="none"> 35 <mapping initial="none">
37 </mapping> 37 </mapping>
38 </sanitizer> 38 </sanitizer>
39 </param> 39 </param>
40 </when> 40 </when>
41 <when value="file" > 41 <when value="file" >
42 <param name="file" type="data" format="txt,tabular,tsv" label="Select a file that contains your list of identifiers" help="" /> 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 your input file contain a header?" /> 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="The column number of your identifiers to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> 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 </when> 45 </when>
46 </conditional> 46 </conditional>
47 <param name="id_type" type="select" label="select your identifiers type :" > 47 <param name="id_type" type="select" label="Select IDs" >
48 <option value="ncbi-geneid" selected="true">Entrez genes ID</option> 48 <option value="ncbi-geneid" selected="true">Entrez Gene ID</option>
49 <option value="kegg-id">KEGG genes ID</option> 49 <option value="kegg-id">KEGG gene ID</option>
50 <option value="uniprot">Uniprot Accession number</option> 50 <option value="uniprot">UniProt Accession number</option>
51 51
52 </param> 52 </param>
53 <param name="species" type="select" label="Select species"> 53 <param name="species" type="select" label="Species">
54 <option value="hsa">Human (H. sapiens)</option> 54 <option value="hsa">Human (Homo sapiens)</option>
55 <option value="mmu">Mouse (M. musculus)</option> 55 <option value="mmu">Mouse (Mus musculus)</option>
56 <option value="rno">Rat (R. norvegicus)</option> 56 <option value="rno">Rat (Rattus norvegicus)</option>
57 </param> 57 </param>
58 <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 <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"/>
59 </inputs> 59 </inputs>
60 <outputs> 60 <outputs>
61 <data name="output1" format="tsv" /> 61 <data name="output1" format="tsv" />
62 </outputs> 62 </outputs>
63 <tests> 63 <tests>
74 <output name="output1" value="test.tsv" /> 74 <output name="output1" value="test.tsv" />
75 </test> 75 </test>
76 </tests> 76 </tests>
77 <help><![CDATA[ 77 <help><![CDATA[
78 78
79 This tool maps a list of identifiers 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 **Description**
80 80
81 It allows you to directly identify the signaling pathways that are the most covered by your proteomics dataset. 81 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.
82 82
83 By default the number of pathway to be displayed is set to 10 and sorted in descending order. 83 It allows you to directly identify KEGG pathways that are the most covered by your gene/protein list.
84 84
85 At the moment three species are supported: Human (Homo sapiens), Mouse (Mus musculus) and Rat (Rattus norvegicus). 85 -----
86 86
87 **Input:** 87 **Input**
88 88
89 Input can be either a list of ids or a file containing multiple columns but with at least one column of ids (e.g. hsa04970). 89 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).
90 Input ids type can be Entrez gene ID, KEGG gene ID or Uniprot accession number. 90 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).
91 91
92 .. class:: warningmark 92 .. class:: warningmark
93 93
94 If you use Uniprot accession number, it will be converted to KEGG gene ID, this step can be time consuming. 94 If you use Uniprot accession number, it will be converted to KEGG gene ID; this step can be time consuming.
95 If your input file contains other type of ids, please use the ID_Converter tool. 95
96 If your input file contains other type of ID, please use the ID_Converter tool.
97
98 -----
99
100 **Parameters**
101
102 "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.
103
104 "Species": three species are supported: Human (Homo sapiens), Mouse (Mus musculus) and Rat (Rattus norvegicus).
105
106 -----
96 107
97 **Output:** 108 **Output:**
98 109
99 The output is a tabular file (.tsv) with the following columns: 110 The output is a tabular file (.tsv) with the following columns:
100 111
101 * **Pathway_ID:** KEGG pathway identifier (e.g. hsa04970) 112 * **Pathway_ID:** KEGG pathway identifier (e.g. hsa04970)
102 * **Description:** name of the pathway as in KEGG 113 * **Description:** name of the pathway as in KEGG
103 * **Ratio IDs mapped/total IDs (%):** percentage of pathway coverage 114 * **Ratio IDs mapped/total IDs (%):** pathway coverage in percentage
104 * **nb KEGG genes IDs mapped in the pathway:** number of KEGG genes of your list mapped on the KEGG pathway 115 * **nb KEGG genes IDs mapped in the pathway:** number of KEGG genes from your list mapped to the KEGG pathway
105 * **nb total of KEGG genes IDs present in the pathway:** total number of KEGG genes present in the KEGG pathway 116 * **nb total of KEGG genes IDs present in the pathway:** total number of KEGG genes present in the KEGG pathway
106 117
107 ----- 118 -----
108 119
109 .. class:: infomark 120 .. class:: infomark
110 121
111 **Database:** 122 **Data source (release date)**
112 123
113 Pathways and KEGG genes IDs are collected via KEGGREST package. 124 Pathways and KEGG genes IDs are collected via KEGGREST package.
114 125
115 User manual / Documentation: KEGGREST Bioconductor package https://bioconductor.org/packages/3.1/bioc/html/KEGGREST.html 126 User manual / Documentation: KEGGREST Bioconductor package https://bioconductor.org/packages/3.1/bioc/html/KEGGREST.html
116
117 127
118 ----- 128 -----
119 129
120 .. class:: infomark 130 .. class:: infomark
121 131
122 **Galaxy integration** 132 **Galaxy integration**
123 133
124 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 134 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
125 135
126 Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform 136 Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
127 137
128 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 138 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
129 139
130 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 140 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
131 141