annotate uniprotxml_downloader.xml @ 1:fc8c4bd28681 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author galaxyp
date Wed, 07 Dec 2016 16:44:14 -0500
parents 0bd2688166a5
children e1abc9a35c64
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1 <tool id="uniprotxml_downloader" name="UniProtXML Download" version="1.0.1">
0
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2 <description>proteome</description>
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3 <requirements>
1
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4 <requirement type="package" version="2.7.12">python</requirement>
0
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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>
1
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9 <command>
0
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10 <![CDATA[
1
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11 python '$__tool_directory__/uniprotxml_downloader.py'
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12 -v
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13 #if $taxid.choice == 'common':
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14 --taxon '$taxid.organism'
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15 #if $taxid.reviewed:
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16 --reviewed=$taxid.reviewed
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17 #end if
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18 #else:
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19 #for id in $taxid.taxons.split(','):
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20 -t $id
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21 #end for
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22 #end if
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23 --output="${proteome}"
0
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24 ]]>
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25 </command>
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26 <inputs>
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27 <conditional name="taxid">
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28 <param name="choice" type="select" label="Select">
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29 <option value="common">A Common Organism</option>
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30 <option value="taxids">By Organism IDs</option>
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31 </param>
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32 <when value="common">
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33 <param name="organism" type="select" label="Common Organisms"
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34 help="select species for protein database">
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35 <options from_file="uniprot_taxons.loc">
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36 <column name="name" index="0" />
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37 <column name="value" index="1" />
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38 </options>
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39 </param>
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40 <param name="reviewed" type="select" label="filter by reviewed status" optional="true">
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41 <help><![CDATA[
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42 UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database that may contain
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43 redundant sequences, but there is a higher chance peptides will be identified.
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44 UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database with
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45 less of a chance peptides will be identified but less sequence redundancy
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46 ]]>
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47 </help>
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48 <option value="yes">UniProtKB/Swiss-Prot (reviewed only)</option>
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49 <option value="no">UniProtKB/TrEMBL (unreviewed only)</option>
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50 </param>
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51 </when>
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52 <when value="taxids">
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53 <param name="taxons" type="text" label="NCBI taxon IDs"
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54 help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/">
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55 <validator type="regex" message="OrganismID[,OrganismID]">^\d+(,\d+)*$</validator>
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56 </param>
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57 </when>
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58 </conditional>
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59 </inputs>
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60 <outputs>
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61 <data format="uniprotxml" name="proteome" label="UniProtXML" />
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62 </outputs>
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63 <tests>
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64 <test>
1
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65 <param name="choice" value="taxids"/>
0
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66 <param name="taxons" value="1566990"/>
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67 <output name="uniprotxml">
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68 <assert_contents>
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69 <has_text text="&lt;/uniprot&gt;" />
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70 </assert_contents>
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71 </output>
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72 </test>
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73 </tests>
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74 <help>
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75 <![CDATA[
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76 **UniProtXML Downloader**
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77
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78 Downloads a UniProtXML file from UniProtKB
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79
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80 The Morpheus proteomics search algorithm can use this format as a search database.
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81
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82 Available proteomes: http://www.uniprot.org/proteomes/
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83
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84 UniProtKB help: http://www.uniprot.org/help/uniprotkb
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85
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86 ]]>
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87 </help>
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88 <citations>
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89 <citation type="doi">10.1093/nar/gku989</citation>
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90 </citations>
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91 </tool>
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92