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annotate dbbuilder.xml @ 7:a94dc3d469cb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit 7480b93ed88eb017041b16e1181a481f7b3334d3
author galaxyp
date Tue, 02 May 2017 08:52:01 -0400
parents 19ee2e85931a
children a85fbebe8b2f
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1 <tool id="dbbuilder" name="Protein Database Downloader" version="0.2.1">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package">gnu-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 database." />
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8 <regex match="ERROR" level="fatal" source="stderr" description="Error downloading database." />
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9 </stdio>
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10 <!-- TODO: escape quotes. -->
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11 <!-- Add NCBI and maxquant contaminants. -->
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12 <!-- http://maxquant.org/contaminants.zip -->
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13 <!-- ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz-->
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14 <command>
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15 <![CDATA[
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16 #if $source.from == "uniprot"
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17 #set $url = 'http://www.uniprot.org/uniprot/?query=taxonomy:"' + str($source.taxon) + '"' + 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 $url = "https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta"
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22 #set $type = "direct"
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23 #elif $source.from == "url"
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24 #set $url = $source.url
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25 #set $type = "direct"
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26 #end if
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27 #if $type =="direct"
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28 wget -nv '$url' -O '${output_database}'
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29 #end if
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30 ]]>
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31 </command>
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32 <inputs>
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33 <conditional name="source">
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34 <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">
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35 <option value="uniprot">UniProtKB</option>
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36 <option value="cRAP">cRAP (contaminants)</option>
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37 <option value="url">Custom URL</option>
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38 </param>
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39 <when value="uniprot">
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40 <param name="taxon" type="select" format="text" help="select species for protein database">
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41 <label>Taxonomy</label>
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42 <options from_file="uniprot_taxons.loc">
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43 <column name="name" index="0" />
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44 <column name="value" index="1" />
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45 </options>
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46 </param>
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47 <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">
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48 <option value="+">UniProtKB</option>
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49 <option value="+reviewed%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option>
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50 <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option>
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51 <sanitizer>
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52 <valid>
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53 <add value="%"/>
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54 </valid>
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55 </sanitizer>
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56 </param>
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57 <param name="set" type="select" label="Proteome Set">
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58 <option value="+">Any</option>
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59 <option value="+keyword%3a1185" selected="true">Reference Proteome Set</option>
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60 <option value="+keyword%3a181">Complete Proteome Set</option>
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61 <sanitizer>
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62 <valid>
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63 <add value="%"/>
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64 </valid>
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65 </sanitizer>
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66 </param>
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67 <param name="include_isoform" type="boolean" truevalue="&amp;include=yes" falsevalue="" label="Include isoform data" help="several different forms of a given protein are incorporated into database" />
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68 </when>
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69 <when value="cRAP" />
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70 <when value="url">
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71 <param name="url" value="" type="text" label="URL (http, ftp)">
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72 <sanitizer>
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73 <valid>
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74 <add value="%"/>
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75 </valid>
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76 </sanitizer>
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77 </param>
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78 </when>
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79 </conditional>
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80 </inputs>
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81 <outputs>
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82 <data format="fasta" name="output_database" label="Protein Database" />
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83 </outputs>
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84 <tests>
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85 <test>
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86 <param name="from" value="cRAP" />
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87 <output name="output_database">
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88 <assert_contents>
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89 <has_text text="KKA1_ECOLX" />
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90 </assert_contents>
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91 </output>
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92 </test>
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93 </tests>
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94 <help>
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95 <![CDATA[
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96 **Output**
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97
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98 Creates a FASTA file of specified protein sequences for comparison with experimental MS/MS data in search algorithm.
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99
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100 **External Links**
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101
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102 _Galaxy-P 101 shows usage Protein Database Downloader tool in the creation of a workflow
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103 .. _Galaxy-P 101: http://msi-galaxy-p.readthedocs.org/en/latest/sections/galaxyp_101.html
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104 _UniProtKB provides additional information about the UniProt Knowledgebase
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105 .. _UniProtKB: http://www.uniprot.org/help/uniprotkb
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106 ]]>
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107 </help>
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108 </tool>
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109