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1 <tool id="dbbuilder" version="0.2.0" name="Protein Database Downloader">
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2 <description>
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3 </description>
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4 <requirements>
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5 <requirement type="binary">wget</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Error downloading database." />
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9 <regex match="ERROR" level="fatal" source="stderr" description="Error downloading database." />
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10 </stdio>
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11 <!-- TODO: escape quotes. -->
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12 <!-- Add NCBI and maxquant contaminants. -->
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13 <!-- http://maxquant.org/contaminants.zip -->
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14 <!-- ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz-->
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15 <command>
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16 #if $source.from == "uniprot"
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17 #set $url = "http://www.uniprot.org/uniprot/?query=taxonomy%3a%22" + str($source.taxon) + "%22" + str($source.set) + str($source.reviewed) + "&force=yes&format=fasta" + str($source.include_isoform)
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18 #set $type = "direct"
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19 #elif $source.from == "cRAP"
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20 #set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta"
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21 #set $type = "direct"
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22 #elif $source.from == "url"
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23 #set $url = $source.url
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24 #set $type = "direct"
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25 #end if
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26 #if $type =="direct"
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27 wget -nv '$url' -O '${output_database}'
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28 #end if
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29 </command>
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30 <inputs>
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31 <conditional name="source">
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32 <param name="from" type="select" label="Download from">
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33 <option value="uniprot">UniProtKB</option>
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34 <option value="cRAP">cRAP (contaminants)</option>
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35 <option value="url">Custom URL</option>
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36 </param>
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37 <when value="uniprot">
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38 <param name="taxon" type="select" format="text" >
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39 <label>Taxonomy</label>
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40 <options from_file="uniprot_taxons.loc">
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41 <column name="name" index="0" />
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42 <column name="value" index="1" />
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43 </options>
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44 </param>
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45 <param name="reviewed" type="select">
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46 <option value="+">UniProtKB</option>
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47 <option value="+reviewed%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option>
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48 <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option>
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49 <sanitizer>
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50 <valid>
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51 <add value="%"/>
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52 </valid>
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53 </sanitizer>
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54 </param>
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55 <param name="set" type="select" label="Proteome Set">
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56 <option value="+">Any</option>
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57 <option value="+keyword%3a1185" selected="true">Reference Proteome Set</option>
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58 <option value="+keyword%3a181">Complete Proteome Set</option>
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59 <sanitizer>
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60 <valid>
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61 <add value="%"/>
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62 </valid>
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63 </sanitizer>
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64 </param>
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65 <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" />
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66 </when>
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67 <when value="cRAP" />
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68 <when value="url">
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69 <param name="url" value="" type="text" label="URL (http, ftp)">
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70 <sanitizer>
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71 <valid>
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72 <add value="%"/>
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73 </valid>
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74 </sanitizer>
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75 </param>
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76 </when>
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77 </conditional>
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78 </inputs>
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79 <outputs>
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80 <data format="fasta" name="output_database" label="Protein Database" />
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81 </outputs>
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82 <help>
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83 **Output**
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84
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85 A FASTA file containing the specified protein sequences.
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86
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87 </help>
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88 </tool>
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89
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