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comparison dbbuilder.xml @ 0:ab1148688233 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
author galaxyp
date Sat, 29 Apr 2017 09:46:11 -0400
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1 <tool id="dbbuilder" name="Protein Database Downloader" version="0.2.1">
2 <description></description>
3 <requirements>
4 <requirement type="package">gnu-wget</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" level="fatal" description="Error downloading database." />
8 <regex match="ERROR" level="fatal" source="stderr" description="Error downloading database." />
9 </stdio>
10 <!-- TODO: escape quotes. -->
11 <!-- Add NCBI and maxquant contaminants. -->
12 <!-- http://maxquant.org/contaminants.zip -->
13 <!-- ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz-->
14 <command>
15 <![CDATA[
16 #if $source.from == "uniprot"
17 #set $url = "http://www.uniprot.org/uniprot/?query=taxonomy%3a%22" + str($source.taxon) + "%22" + str($source.set) + str($source.reviewed) + "&amp;force=yes&amp;format=fasta" + str($source.include_isoform)
18 #set $type = "direct"
19 #elif $source.from == "cRAP"
20 ##set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta"
21 #set $url = "https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta"
22 #set $type = "direct"
23 #elif $source.from == "url"
24 #set $url = $source.url
25 #set $type = "direct"
26 #end if
27 #if $type =="direct"
28 wget -nv '$url' -O '${output_database}'
29 #end if
30 ]]>
31 </command>
32 <inputs>
33 <conditional name="source">
34 <param name="from" type="select" label="Download from" help="Select database source. cRAP acts as a database for common MS contaminants. UniProtKB is a corss species collection of functional protein databases">
35 <option value="uniprot">UniProtKB</option>
36 <option value="cRAP">cRAP (contaminants)</option>
37 <option value="url">Custom URL</option>
38 </param>
39 <when value="uniprot">
40 <param name="taxon" type="select" format="text" help="select species for protein database">
41 <label>Taxonomy</label>
42 <options from_file="uniprot_taxons.loc">
43 <column name="name" index="0" />
44 <column name="value" index="1" />
45 </options>
46 </param>
47 <param name="reviewed" type="select" help="UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database- may contain redundant sequences, but there is a higher chance peptides will be identified. UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database- less of a chance peptides will be identified but less sequence redundancy">
48 <option value="+">UniProtKB</option>
49 <option value="+reviewed%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option>
50 <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option>
51 <sanitizer>
52 <valid>
53 <add value="%"/>
54 </valid>
55 </sanitizer>
56 </param>
57 <param name="set" type="select" label="Proteome Set">
58 <option value="+">Any</option>
59 <option value="+keyword%3a1185" selected="true">Reference Proteome Set</option>
60 <option value="+keyword%3a181">Complete Proteome Set</option>
61 <sanitizer>
62 <valid>
63 <add value="%"/>
64 </valid>
65 </sanitizer>
66 </param>
67 <param name="include_isoform" type="boolean" truevalue="&amp;include=yes" falsevalue="" label="Include isoform data" help="several different forms of a given protein are incorporated into database" />
68 </when>
69 <when value="cRAP" />
70 <when value="url">
71 <param name="url" value="" type="text" label="URL (http, ftp)">
72 <sanitizer>
73 <valid>
74 <add value="%"/>
75 </valid>
76 </sanitizer>
77 </param>
78 </when>
79 </conditional>
80 </inputs>
81 <outputs>
82 <data format="fasta" name="output_database" label="Protein Database" />
83 </outputs>
84 <tests>
85 <test>
86 <param name="from" value="cRAP" />
87 <output name="output_database">
88 <assert_contents>
89 <has_text text="KKA1_ECOLX" />
90 </assert_contents>
91 </output>
92 </test>
93 </tests>
94 <help>
95 <![CDATA[
96 **Output**
97
98 Creates a FASTA file of specified protein sequences for comparison with experimental MS/MS data in search algorithm.
99
100 **External Links**
101
102 _Galaxy-P 101 shows usage Protein Database Downloader tool in the creation of a workflow
103 .. _Galaxy-P 101: http://msi-galaxy-p.readthedocs.org/en/latest/sections/galaxyp_101.html
104 _UniProtKB provides additional information about the UniProt Knowledgebase
105 .. _UniProtKB: http://www.uniprot.org/help/uniprotkb
106 ]]>
107 </help>
108 </tool>
109