Mercurial > repos > galaxyp > uniprotxml_downloader

annotate uniprotxml_downloader.xml @ 0:0bd2688166a5 draft

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