Mercurial > repos > galaxyp > dbbuilder
comparison dbbuilder.xml @ 3:a38cd98a6b41 draft
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author | galaxyp |
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date | Fri, 12 Jul 2013 12:57:50 -0400 |
parents | 6c624803c5f9 |
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2:6c624803c5f9 | 3:a38cd98a6b41 |
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27 wget -nv '$url' -O '${output_database}' | 27 wget -nv '$url' -O '${output_database}' |
28 #end if | 28 #end if |
29 </command> | 29 </command> |
30 <inputs> | 30 <inputs> |
31 <conditional name="source"> | 31 <conditional name="source"> |
32 <param name="from" type="select" label="Download from"> | 32 <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"> |
33 <option value="uniprot">UniProtKB</option> | 33 <option value="uniprot">UniProtKB</option> |
34 <option value="cRAP">cRAP (contaminants)</option> | 34 <option value="cRAP">cRAP (contaminants)</option> |
35 <option value="url">Custom URL</option> | 35 <option value="url">Custom URL</option> |
36 </param> | 36 </param> |
37 <when value="uniprot"> | 37 <when value="uniprot"> |
38 <param name="taxon" type="select" format="text" > | 38 <param name="taxon" type="select" format="text" help="select species for protein database"> |
39 <label>Taxonomy</label> | 39 <label>Taxonomy</label> |
40 <options from_file="uniprot_taxons.loc"> | 40 <options from_file="uniprot_taxons.loc"> |
41 <column name="name" index="0" /> | 41 <column name="name" index="0" /> |
42 <column name="value" index="1" /> | 42 <column name="value" index="1" /> |
43 </options> | 43 </options> |
44 </param> | 44 </param> |
45 <param name="reviewed" type="select"> | 45 <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"> |
46 <option value="+">UniProtKB</option> | 46 <option value="+">UniProtKB</option> |
47 <option value="+reviewed%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option> | 47 <option value="+reviewed%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option> |
48 <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option> | 48 <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option> |
49 <sanitizer> | 49 <sanitizer> |
50 <valid> | 50 <valid> |
60 <valid> | 60 <valid> |
61 <add value="%"/> | 61 <add value="%"/> |
62 </valid> | 62 </valid> |
63 </sanitizer> | 63 </sanitizer> |
64 </param> | 64 </param> |
65 <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" /> | 65 <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" help="several different forms of a given protein are incorporated into database" /> |
66 </when> | 66 </when> |
67 <when value="cRAP" /> | 67 <when value="cRAP" /> |
68 <when value="url"> | 68 <when value="url"> |
69 <param name="url" value="" type="text" label="URL (http, ftp)"> | 69 <param name="url" value="" type="text" label="URL (http, ftp)"> |
70 <sanitizer> | 70 <sanitizer> |
80 <data format="fasta" name="output_database" label="Protein Database" /> | 80 <data format="fasta" name="output_database" label="Protein Database" /> |
81 </outputs> | 81 </outputs> |
82 <help> | 82 <help> |
83 **Output** | 83 **Output** |
84 | 84 |
85 A FASTA file containing the specified protein sequences. | 85 Creates a FASTA file of specified protein sequences for comparison with experimental MS/MS data in search algorithm. |
86 | 86 |
87 **External Links** | |
88 | |
89 _Galaxy-P 101 shows usage Protein Database Downloader tool in the creation of a workflow | |
90 .. _Galaxy-P 101: http://msi-galaxy-p.readthedocs.org/en/latest/sections/galaxyp_101.html | |
91 _UniProtKB provides additional information about the UniProt Knowledgebase | |
92 .. _UniProtKB: http://www.uniprot.org/help/uniprotkb | |
87 </help> | 93 </help> |
88 </tool> | 94 </tool> |
89 | 95 |