Mercurial > repos > galaxyp > uniprotxml_downloader
comparison uniprotxml_downloader.xml @ 0:0bd2688166a5 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
| author | galaxyp |
|---|---|
| date | Tue, 08 Mar 2016 12:03:49 -0500 |
| parents | |
| children | fc8c4bd28681 |
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| -1:000000000000 | 0:0bd2688166a5 |
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| 1 <tool id="uniprotxml_downloader" name="UniProtXML Download" version="1.0.0"> | |
| 2 <description>proteome</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">wget</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" level="fatal" description="Error downloading proteome." /> | |
| 8 </stdio> | |
| 9 <command interpreter="python"> | |
| 10 <![CDATA[ | |
| 11 uniprotxml_downloader.py -v | |
| 12 #if $taxid.choice == 'common': | |
| 13 --taxon $taxid.organism | |
| 14 #if $taxid.reviewed: | |
| 15 --reviewed=$taxid.reviewed | |
| 16 #end if | |
| 17 #else: | |
| 18 #for id in $taxid.taxons.split(','): | |
| 19 -t $id | |
| 20 #end for | |
| 21 #end if | |
| 22 --output="${proteome}" | |
| 23 ]]> | |
| 24 </command> | |
| 25 <inputs> | |
| 26 <conditional name="taxid"> | |
| 27 <param name="choice" type="select" label="Select"> | |
| 28 <option value="common">A Common Organism</option> | |
| 29 <option value="taxids">By Organism IDs</option> | |
| 30 </param> | |
| 31 <when value="common"> | |
| 32 <param name="organism" type="select" label="Common Organisms" | |
| 33 help="select species for protein database"> | |
| 34 <options from_file="uniprot_taxons.loc"> | |
| 35 <column name="name" index="0" /> | |
| 36 <column name="value" index="1" /> | |
| 37 </options> | |
| 38 </param> | |
| 39 <param name="reviewed" type="select" label="filter by reviewed status" optional="true"> | |
| 40 <help><![CDATA[ | |
| 41 UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database that may contain | |
| 42 redundant sequences, but there is a higher chance peptides will be identified. | |
| 43 UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database with | |
| 44 less of a chance peptides will be identified but less sequence redundancy | |
| 45 ]]> | |
| 46 </help> | |
| 47 <option value="yes">UniProtKB/Swiss-Prot (reviewed only)</option> | |
| 48 <option value="no">UniProtKB/TrEMBL (unreviewed only)</option> | |
| 49 </param> | |
| 50 </when> | |
| 51 <when value="taxids"> | |
| 52 <param name="taxons" type="text" label="NCBI taxon IDs" | |
| 53 help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/"> | |
| 54 <validator type="regex" message="OrganismID[,OrganismID]">^\d+(,\d+)*$</validator> | |
| 55 </param> | |
| 56 </when> | |
| 57 </conditional> | |
| 58 </inputs> | |
| 59 <outputs> | |
| 60 <data format="uniprotxml" name="proteome" label="UniProtXML" /> | |
| 61 </outputs> | |
| 62 <tests> | |
| 63 <test> | |
| 64 <param name="taxons" value="1566990"/> | |
| 65 <output name="uniprotxml"> | |
| 66 <assert_contents> | |
| 67 <has_text text="</uniprot>" /> | |
| 68 </assert_contents> | |
| 69 </output> | |
| 70 </test> | |
| 71 </tests> | |
| 72 <help> | |
| 73 <![CDATA[ | |
| 74 **UniProtXML Downloader** | |
| 75 | |
| 76 Downloads a UniProtXML file from UniProtKB | |
| 77 | |
| 78 The Morpheus proteomics search algorithm can use this format as a search database. | |
| 79 | |
| 80 Available proteomes: http://www.uniprot.org/proteomes/ | |
| 81 | |
| 82 UniProtKB help: http://www.uniprot.org/help/uniprotkb | |
| 83 | |
| 84 ]]> | |
| 85 </help> | |
| 86 <citations> | |
| 87 <citation type="doi">10.1093/nar/gku989</citation> | |
| 88 </citations> | |
| 89 </tool> | |
| 90 |