Mercurial > repos > galaxyp > uniprotxml_downloader

annotate uniprotxml_downloader.xml @ 3:1a5690a5eedc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 6aac77a68426533c8c18c9f6aabd2df56a82de24
author galaxyp
date Tue, 02 Jul 2019 21:46:14 -0400
parents e1abc9a35c64
children 12692567c7f9
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1 <tool id="uniprotxml_downloader" name="UniProt" version="2.1.0">
2
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2 <description>download proteome as XML or fasta</description>
0
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3 <requirements>
2
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4 <requirement type="package" version="2.7">python</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>
0
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10 <![CDATA[
2
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11 python $__tool_directory__/uniprotxml_downloader.py -v
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12 #if $taxid.input_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 #elif $taxid.input_choice == 'taxids':
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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 #elif $taxid.input_choice == 'history':
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22 --input="${taxid.taxon_file}"
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23 --column=#echo int(str($taxid.column)) - 1#
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24 #end if
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25 --format=$format
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26 --output="${proteome}"
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27 ]]>
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28 </command>
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29 <inputs>
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30 <conditional name="taxid">
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31 <param name="input_choice" type="select" label="Select">
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32 <option value="common">A Common Organism</option>
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33 <option value="taxids">By Organism IDs</option>
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34 <option value="history">A history dataset with an Organism Taxonomy Name column</option>
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35 </param>
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36 <when value="common">
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37 <param name="organism" type="select" label="Common Organisms"
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38 help="select species for protein database">
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39 <options from_file="uniprot_taxons.loc">
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40 <column name="name" index="0" />
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41 <column name="value" index="1" />
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42 </options>
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43 </param>
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44 <param name="reviewed" type="select" label="filter by reviewed status" optional="true">
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45 <help><![CDATA[
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46 UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database that may contain
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47 redundant sequences, but there is a higher chance peptides will be identified.
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48 UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database with
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49 less of a chance peptides will be identified but less sequence redundancy
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50 ]]>
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51 </help>
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52 <option value="yes">UniProtKB/Swiss-Prot (reviewed only)</option>
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53 <option value="no">UniProtKB/TrEMBL (unreviewed only)</option>
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54 </param>
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55 </when>
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56 <when value="taxids">
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57 <param name="taxons" type="text" label="NCBI Taxon IDs or names"
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58 help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/">
2
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59 <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator>
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60 </param>
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61 </when>
2
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62 <when value="history">
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63 <param name="taxon_file" type="data" format="tabular" label="Dataset with Taxon Name column"/>
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64 <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon name"/>
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65 </when>
0
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66 </conditional>
2
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67 <param name="format" type="select" label="uniprot output format">
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68 <option value="xml">xml</option>
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69 <option value="fasta">fasta</option>
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70 </param>
0
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71 </inputs>
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72 <outputs>
2
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73 <data format="uniprotxml" name="proteome" label="UniProt.${format}">
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74 <change_format>
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75 <when input="format" value="fasta" format="fasta" />
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76 </change_format>
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77 </data>
0
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78 </outputs>
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79 <tests>
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80 <test>
2
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81 <param name="input_choice" value="taxids"/>
0
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82 <param name="taxons" value="1566990"/>
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83 <param name="format" value="xml"/>
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84 <output name="proteome">
0
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85 <assert_contents>
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86 <has_text text="&lt;/uniprot&gt;" />
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87 </assert_contents>
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88 </output>
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89 </test>
2
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90 <test>
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91 <param name="input_choice" value="taxids"/>
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92 <param name="taxons" value="Shi470,PeCan4"/>
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93 <param name="format" value="fasta"/>
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94 <output name="proteome">
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95 <assert_contents>
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96 <has_text text="Shi470" />
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97 <has_text text="PeCan4" />
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98 </assert_contents>
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99 </output>
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100 </test>
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101 <test>
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102 <param name="input_choice" value="history"/>
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103 <param name="taxon_file" value="Helicobacter_strains.tsv" ftype="tabular"/>
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104 <param name="column" value="1"/>
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105 <param name="format" value="fasta"/>
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106 <output name="proteome">
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107 <assert_contents>
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108 <has_text text="Shi470" />
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109 <has_text text="PeCan4" />
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110 </assert_contents>
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111 </output>
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112 </test>
0
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113 </tests>
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114 <help>
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115 <![CDATA[
2
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116 **UniProt Downloader**
0
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117
2
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118 Downloads either a UniProtXML file or a fasta file from UniProtKB
0
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119
2
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120 The Morpheus proteomics search algorithm can use the UniProtXML format as a search database.
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121
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122 Available proteomes: http://www.uniprot.org/proteomes/
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123
2
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124 Available taxon names: http://www.uniprot.org/taxonomy/
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125
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126 Example taxon: http://www.uniprot.org/taxonomy/512562
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127
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128 Taxon IDs or names can be entered as text or read from a column in a tabular dataset from your history.
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129
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130 Example IDs and names releated to the Bacteria Helicobacter pylori (strain Shi470) ::
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131
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132
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133 - 512562
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134 - Shi470
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135 - Helicobacter pylori
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136 - Helicobacter
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137 - Helicobacteraceae
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138
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139
0
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140 UniProtKB help: http://www.uniprot.org/help/uniprotkb
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141
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142 ]]>
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143 </help>
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144 <citations>
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145 <citation type="doi">10.1093/nar/gku989</citation>
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146 </citations>
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147 </tool>
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148