Mercurial > repos > galaxyp > uniprotxml_downloader

comparison uniprotxml_downloader.xml @ 2:e1abc9a35c64 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
author galaxyp
date Fri, 16 Dec 2016 17:33:05 -0500
parents fc8c4bd28681
children 1a5690a5eedc
comparison
equal deleted inserted replaced
1:fc8c4bd28681 2:e1abc9a35c64
1 <tool id="uniprotxml_downloader" name="UniProtXML Download" version="1.0.1"> 1 <tool id="uniprotxml_downloader" name="UniProt" version="2.0.0">
2 <description>proteome</description> 2 <description>download proteome as XML or fasta</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.7.12">python</requirement> 4 <requirement type="package" version="2.7">python</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" level="fatal" description="Error downloading proteome." /> 7 <exit_code range="1:" level="fatal" description="Error downloading proteome." />
8 </stdio> 8 </stdio>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 python '$__tool_directory__/uniprotxml_downloader.py' 11 python $__tool_directory__/uniprotxml_downloader.py -v
12 -v 12 #if $taxid.input_choice == 'common':
13 #if $taxid.choice == 'common': 13 --taxon $taxid.organism
14 --taxon '$taxid.organism' 14 #if $taxid.reviewed:
15 #if $taxid.reviewed: 15 --reviewed=$taxid.reviewed
16 --reviewed=$taxid.reviewed 16 #end if
17 #end if 17 #elif $taxid.input_choice == 'taxids':
18 #else: 18 #for $id in $taxid.taxons.split(','):
19 #for id in $taxid.taxons.split(','): 19 -t "$id"
20 -t $id 20 #end for
21 #end for 21 #elif $taxid.input_choice == 'history':
22 #end if 22 --input="${taxid.taxon_file}"
23 --output="${proteome}" 23 --column=#echo int(str($taxid.column)) - 1#
24 #end if
25 --format=$format
26 --output="${proteome}"
24 ]]> 27 ]]>
25 </command> 28 </command>
26 <inputs> 29 <inputs>
27 <conditional name="taxid"> 30 <conditional name="taxid">
28 <param name="choice" type="select" label="Select"> 31 <param name="input_choice" type="select" label="Select">
29 <option value="common">A Common Organism</option> 32 <option value="common">A Common Organism</option>
30 <option value="taxids">By Organism IDs</option> 33 <option value="taxids">By Organism IDs</option>
34 <option value="history">A history dataset with an Organism Taxonomy Name column</option>
31 </param> 35 </param>
32 <when value="common"> 36 <when value="common">
33 <param name="organism" type="select" label="Common Organisms" 37 <param name="organism" type="select" label="Common Organisms"
34 help="select species for protein database"> 38 help="select species for protein database">
35 <options from_file="uniprot_taxons.loc"> 39 <options from_file="uniprot_taxons.loc">
48 <option value="yes">UniProtKB/Swiss-Prot (reviewed only)</option> 52 <option value="yes">UniProtKB/Swiss-Prot (reviewed only)</option>
49 <option value="no">UniProtKB/TrEMBL (unreviewed only)</option> 53 <option value="no">UniProtKB/TrEMBL (unreviewed only)</option>
50 </param> 54 </param>
51 </when> 55 </when>
52 <when value="taxids"> 56 <when value="taxids">
53 <param name="taxons" type="text" label="NCBI taxon IDs" 57 <param name="taxons" type="text" label="NCBI Taxon IDs or names"
54 help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/"> 58 help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/">
55 <validator type="regex" message="OrganismID[,OrganismID]">^\d+(,\d+)*$</validator> 59 <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator>
56 </param> 60 </param>
57 </when> 61 </when>
62 <when value="history">
63 <param name="taxon_file" type="data" format="tabular" label="Dataset with Taxon Name column"/>
64 <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon name"/>
65 </when>
58 </conditional> 66 </conditional>
67 <param name="format" type="select" label="uniprot output format">
68 <option value="xml">xml</option>
69 <option value="fasta">fasta</option>
70 </param>
59 </inputs> 71 </inputs>
60 <outputs> 72 <outputs>
61 <data format="uniprotxml" name="proteome" label="UniProtXML" /> 73 <data format="uniprotxml" name="proteome" label="UniProt.${format}">
74 <change_format>
75 <when input="format" value="fasta" format="fasta" />
76 </change_format>
77 </data>
62 </outputs> 78 </outputs>
63 <tests> 79 <tests>
64 <test> 80 <test>
65 <param name="choice" value="taxids"/> 81 <param name="input_choice" value="taxids"/>
66 <param name="taxons" value="1566990"/> 82 <param name="taxons" value="1566990"/>
67 <output name="uniprotxml"> 83 <param name="format" value="xml"/>
84 <output name="proteome">
68 <assert_contents> 85 <assert_contents>
69 <has_text text="&lt;/uniprot&gt;" /> 86 <has_text text="&lt;/uniprot&gt;" />
87 </assert_contents>
88 </output>
89 </test>
90 <test>
91 <param name="input_choice" value="taxids"/>
92 <param name="taxons" value="Shi470,PeCan4"/>
93 <param name="format" value="fasta"/>
94 <output name="proteome">
95 <assert_contents>
96 <has_text text="Shi470" />
97 <has_text text="PeCan4" />
98 </assert_contents>
99 </output>
100 </test>
101 <test>
102 <param name="input_choice" value="history"/>
103 <param name="taxon_file" value="Helicobacter_strains.tsv" ftype="tabular"/>
104 <param name="column" value="1"/>
105 <param name="format" value="fasta"/>
106 <output name="proteome">
107 <assert_contents>
108 <has_text text="Shi470" />
109 <has_text text="PeCan4" />
70 </assert_contents> 110 </assert_contents>
71 </output> 111 </output>
72 </test> 112 </test>
73 </tests> 113 </tests>
74 <help> 114 <help>
75 <![CDATA[ 115 <![CDATA[
76 **UniProtXML Downloader** 116 **UniProt Downloader**
77 117
78 Downloads a UniProtXML file from UniProtKB 118 Downloads either a UniProtXML file or a fasta file from UniProtKB
79 119
80 The Morpheus proteomics search algorithm can use this format as a search database. 120 The Morpheus proteomics search algorithm can use the UniProtXML format as a search database.
81 121
82 Available proteomes: http://www.uniprot.org/proteomes/ 122 Available proteomes: http://www.uniprot.org/proteomes/
123
124 Available taxon names: http://www.uniprot.org/taxonomy/
125
126 Example taxon: http://www.uniprot.org/taxonomy/512562
127
128 Taxon IDs or names can be entered as text or read from a column in a tabular dataset from your history.
129
130 Example IDs and names releated to the Bacteria Helicobacter pylori (strain Shi470) ::
131
132
133 - 512562
134 - Shi470
135 - Helicobacter pylori
136 - Helicobacter
137 - Helicobacteraceae
138
83 139
84 UniProtKB help: http://www.uniprot.org/help/uniprotkb 140 UniProtKB help: http://www.uniprot.org/help/uniprotkb
85 141
86 ]]> 142 ]]>
87 </help> 143 </help>