Mercurial > repos > galaxyp > uniprotxml_downloader

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
author galaxyp
date Thu, 06 Jul 2023 21:15:39 +0000
parents 265c35540faa
children
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a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
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1 <tool id="uniprotxml_downloader" name="UniProt" version="2.4.0" profile="21.01">
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2 <description>download proteome as XML or fasta</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="2.25.1">requests</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" description="Error downloading proteome." />
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11 </stdio>
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12 <command>
0
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13 <![CDATA[
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14 python '$__tool_directory__/uniprotxml_downloader.py'
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15 #if $input_method.input_choice == 'common':
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16 --search-id $input_method.organism
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17 --field taxonomy_id
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18 #if $input_method.reviewed:
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19 --reviewed=$input_method.reviewed
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20 #end if
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21 #elif $input_method.input_choice == 'enter_ids':
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22 --field $input_method.field
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23 #for $id in $input_method.ids.split(','):
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24 --search-id '$id'
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25 #end for
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26 #elif $input_method.input_choice == 'history':
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27 --field $input_method.field
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28 --input='${input_method.id_file}'
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29 --column=#echo int(str($input_method.column)) - 1#
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30 #end if
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31 --format $format
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32 --output '${proteome}'
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33 ]]>
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34 </command>
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35 <inputs>
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36 <conditional name="input_method">
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37 <param name="input_choice" type="select" label="Select">
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38 <option value="common">A Common Organism</option>
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39 <option value="enter_ids">A manually entered list of Uniprot IDs</option>
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40 <option value="history">A history dataset with a column containing Uniprot IDs</option>
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41 </param>
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42 <when value="common">
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43 <param name="organism" type="select" label="Common Organisms"
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44 help="select species for protein database">
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45 <options from_file="uniprot_taxons.loc">
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46 <column name="name" index="0" />
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47 <column name="value" index="1" />
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48 </options>
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49 </param>
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50 <param name="reviewed" type="select" label="filter by reviewed status" optional="true">
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51 <help><![CDATA[
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52 UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database that may contain
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53 redundant sequences, but there is a higher chance peptides will be identified.
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54 UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database with
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55 less of a chance peptides will be identified but less sequence redundancy
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56 ]]>
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57 </help>
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58 <option value="yes">UniProtKB/Swiss-Prot (reviewed only)</option>
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59 <option value="no">UniProtKB/TrEMBL (unreviewed only)</option>
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60 </param>
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61 </when>
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62 <when value="enter_ids">
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63 <param name="ids" type="text" label="Search ID values"
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64 help="Enter one or more IDs (separated by commas) from http://www.uniprot.org/proteomes/">
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65 <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator>
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66 </param>
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67 <expand macro="query_field"/>
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68 </when>
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69 <when value="history">
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70 <param name="id_file" type="data" format="tabular,txt" label="Dataset (tab separated) with ID column"/>
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71 <param name="column" type="data_column" data_ref="id_file" label="Column with ID"/>
5
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72 <expand macro="query_field"/>
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73 </when>
0
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74 </conditional>
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75 <param name="format" type="select" label="uniprot output format">
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76 <option value="xml">xml</option>
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77 <option value="fasta">fasta</option>
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78 </param>
0
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79 </inputs>
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80 <outputs>
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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81 <data format="uniprotxml" name="proteome" label="UniProt.${format}">
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82 <change_format>
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83 <when input="format" value="fasta" format="fasta" />
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84 </change_format>
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85 </data>
0
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86 </outputs>
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87 <tests>
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88 <test>
6
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89 <param name="input_choice" value="enter_ids"/>
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90 <param name="ids" value="1566990"/>
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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91 <param name="format" value="xml"/>
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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92 <output name="proteome">
0
0bd2688166a5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
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93 <assert_contents>
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94 <has_text text="&lt;/uniprot&gt;" />
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95 </assert_contents>
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96 </output>
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97 </test>
2
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98 <test>
6
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99 <param name="input_choice" value="enter_ids"/>
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100 <param name="ids" value="765963,512562"/>
5
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101 <param name="field" value="taxonomy_id"/>
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102 <param name="format" value="fasta"/>
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103 <output name="proteome">
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104 <assert_contents>
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galaxyp
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105 <has_text text="Shi470" />
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
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106 <has_text text="PeCan4" />
265c35540faa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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107 </assert_contents>
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108 </output>
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109 </test>
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110 <test>
6
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111 <param name="input_choice" value="enter_ids"/>
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112 <param name="ids" value="Shi470,PeCan4"/>
5
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113 <param name="field" value="taxonomy_name"/>
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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114 <param name="format" value="fasta"/>
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115 <output name="proteome">
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116 <assert_contents>
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117 <has_text text="Shi470" />
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galaxyp
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118 <has_text text="PeCan4" />
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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119 </assert_contents>
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120 </output>
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121 </test>
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122 <test>
6
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123 <param name="input_choice" value="enter_ids"/>
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124 <param name="ids" value="E1Q2I0,E1Q3C4"/>
a371252a2cf6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
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125 <param name="field" value="accession"/>
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126 <param name="format" value="fasta"/>
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127 <output name="proteome">
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128 <assert_contents>
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129 <has_text text="E1Q2I0" />
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130 <has_text text="E1Q3C4" />
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131 </assert_contents>
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132 </output>
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133 </test>
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134 <test>
2
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135 <param name="input_choice" value="history"/>
6
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136 <param name="id_file" value="Helicobacter_strains.tsv" ftype="tabular"/>
2
e1abc9a35c64 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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137 <param name="column" value="1"/>
5
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138 <param name="field" value="taxonomy_name"/>
2
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139 <param name="format" value="fasta"/>
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140 <output name="proteome">
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141 <assert_contents>
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142 <has_text text="Shi470" />
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143 <has_text text="PeCan4" />
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144 </assert_contents>
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145 </output>
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146 </test>
4
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147 <test>
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148 <param name="input_choice" value="history"/>
6
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149 <param name="id_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/>
4
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150 <param name="column" value="2"/>
5
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151 <param name="field" value="taxonomy_id"/>
4
12692567c7f9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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152 <param name="format" value="fasta"/>
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153 <output name="proteome">
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154 <assert_contents>
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155 <has_text text="Shi470" />
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156 <has_text text="PeCan4" />
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157 </assert_contents>
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158 </output>
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159 </test>
6
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160 <test>
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161 <param name="input_choice" value="history"/>
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162 <param name="id_file" value="Helicobacter_protein_accessions.tsv" ftype="tabular"/>
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163 <param name="column" value="1"/>
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164 <param name="field" value="accession"/>
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165 <param name="format" value="fasta"/>
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166 <output name="proteome">
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167 <assert_contents>
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168 <has_text text="E1Q2I0" />
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169 <has_text text="E1Q3C4" />
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170 </assert_contents>
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171 </output>
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172 </test>
0
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173 </tests>
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174 <help>
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175 <![CDATA[
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176 **UniProt Downloader**
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177
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178 Downloads either a UniProtXML file or a fasta file from UniProtKB
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179
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180 The Morpheus proteomics search algorithm can use the UniProtXML format as a search database.
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181
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182 Available proteomes: http://www.uniprot.org/proteomes/
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183
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184 Available taxon names: http://www.uniprot.org/taxonomy/
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185
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186 Example taxon: http://www.uniprot.org/taxonomy/512562
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187
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188 Example protein: https://www.uniprot.org/uniprotkb/E1Q2I0/entry
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189
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190 Description of query fields: https://www.uniprot.org/help/query-fields
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191
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192 IDs can be entered as text or read from a column in a tabular dataset from your history.
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193
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194 Example IDs and names releated to the Bacteria Helicobacter pylori (strain Shi470) ::
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195
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196
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197 - 512562
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198 - Shi470
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199 - Helicobacter pylori
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200 - Helicobacter
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201 - Helicobacteraceae
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202
6
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203 Example protein accession numbers from Helicobacter pylori:
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204
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205 - E1Q2I0
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206 - E1Q3C4
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207
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208
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209 UniProtKB help: http://www.uniprot.org/help/uniprotkb
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210
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211 ]]>
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212 </help>
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213 <citations>
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214 <citation type="doi">10.1093/nar/gku989</citation>
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215 </citations>
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216 </tool>
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217