Mercurial > repos > iuc > ebi_metagenomics_run_downloader

annotate ebi_metagenomics_run_downloader.xml @ 2:6155fa39a899 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
author iuc
date Sat, 21 Jan 2017 14:40:54 -0500
parents e2e9fae080ad
children
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e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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1 <tool id="ebi_metagenomics_run_downloader" name="Download run data" version="0.1.0">
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2 <description>from EBI Metagenomics database</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements">
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9 <requirement type="package" version="7.49.0">curl</requirement>
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10 </expand>
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e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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12 <command detect_errors="exit_code"><![CDATA[
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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13 '$__tool_directory__/download_ebi_metagenomics_run_data'
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14 '$__tool_directory__/ebeye_urllib.py'
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15 '$run_id'
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16 '$information.type'
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17 '$information.to_download'
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19 #if ( $information.type == 'sequences' and $information.to_download != 'ncRNA-tRNA-FASTA') or ($information.type == 'function' and $information.to_download == 'InterProScan')
e2e9fae080ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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20 'multiple_chunks'
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21 #else
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22 'single_chunk'
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23 #end if
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25 'output.dat'
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26 ]]></command>
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27
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28 <inputs>
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29 <param name="run_id" type="text" label="Identifiant of the run in EBI Metagenomics" />
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30
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31 <conditional name="information">
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32 <param name="type" type="select" label="Type of information to download">
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33 <option value="sequences" selected="true">Sequence data</option>
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34 <option value="qc-stats">Quality control statistics</option>
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35 <option value="taxonomy">Taxonomic analysis</option>
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36 <option value="function">Functional analysis</option>
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37 </param>
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38
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39 <when value="sequences">
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40 <param name="to_download" type="select" label="Sequences to download">
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41 <option value="ProcessedReads" selected="true">Processed nucleotide reads</option>
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42 <option value="ReadsWithPredictedCDS">Processed reads with pCDS</option>
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43 <option value="ReadsWithMatches">Processed reads with annotation</option>
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44 <option value="ReadsWithoutMatches">Processed reads without annotation</option>
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45 <option value="PredictedCDSWithAnnotation">Predicted CDS with annotation</option>
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46 <option value="PredictedCDSWithoutAnnotation">Predicted CDS without annotation</option>
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47 <option value="PredictedORFWithoutAnnotation">Predicted ORF without annotation</option>
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48 <option value="ncRNA-tRNA-FASTA">Predicted tRNAs</option>
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49 </param>
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50 </when>
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51
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52 <when value="qc-stats">
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53 <param name="to_download" type="select" label="Quality control statistics to download">
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54 <option value="summary" selected="true">Number of sequence reads per Quality Control step</option>
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55 <option value="stats">Quality control statistics</option>
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56 <option value="length">Read length distribution</option>
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57 <option value="gc_bin">Read GC distribution</option>
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58 <option value="base">Nucleotide position distribution</option>
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59 </param>
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60 </when>
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61
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62 <when value="taxonomy">
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63 <param name="to_download" type="select" label="Taxonomic analysis to download">
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64 <option value="5S-rRNA-FASTA" selected="true">Reads encoding 5S rRNA</option>
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65 <option value="16S-rRNA-FASTA">Reads encoding 16S rRNA</option>
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66 <option value="23S-rRNA-FASTA">Reads encoding 23S rRNA</option>
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67 <option value="OTU-TSV">OTUs, reads and taxonomic assignments (TSV)</option>
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68 <option value="NewickPrunedTree">Phylogenetic tree</option>
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69 </param>
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70 </when>
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71
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72 <when value="function">
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73 <param name="to_download" type="select" label="Functional analysis to download">
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74 <option value="InterProScan" selected="true">InterPro matches</option>
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75 <option value="GOAnnotations">Complete GO annotation</option>
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76 <option value="GOSlimAnnotations">GO slim annotation</option>
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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
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82 <outputs>
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83 <data name="output_file_fasta" format="fasta" label="${tool.name} for ${run_id}" from_work_dir="output.dat">
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84 <filter>( information['type'] == 'sequences' or
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85 ( information['type'] == 'taxonomy' and ( information['to_download'] == '5S-rRNA-FASTA' or
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86 information['to_download'] == '16S-rRNA-FASTA' or information['to_download'] == '23S-rRNA-FASTA' )))
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87 </filter>
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88 </data>
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89 <data name="output_file_tsv" format="tsv" label="${tool.name} for ${run_id}" from_work_dir="output.dat">
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90 <filter>( information['type'] == 'qc-stats' or
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91 ( information['type'] == 'taxonomy' and information['to_download'] == 'OTU-TSV' ) or
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92 ( information['type'] == 'function' and information['to_download'] == 'InterProScan/chunks/1' ))
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93 </filter>
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94 </data>
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95 <data name="output_file_csv" format="csv" label="${tool.name} for ${run_id}" from_work_dir="output.dat">
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96 <filter>( information['type'] == 'function' and ( information['to_download'] == 'GOAnnotations' or information['to_download'] == 'GOSlimAnnotations' ))
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97 </filter>
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98 </data>
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99 <data name="output_file_newick" format="newick" label="${tool.name} for ${run_id}" from_work_dir="output.dat">
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100 <filter>( information['type'] == 'taxonomy' and information['to_download'] == 'NewickPrunedTree')
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101 </filter>
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102 </data>
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103 </outputs>
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104
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105 <tests>
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106 <test>
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107 <param name="run_id" value="ERR675640" />
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108 <conditional name="information">
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109 <param name="type" value="qc-stats" />
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110 <param name="to_download" value="stats" />
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111 </conditional>
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112 <output name="output_file_tsv" file="ERR675640_qc-stats_stats" />
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113 </test>
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114 <test>
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115 <param name="run_id" value="ERR675573" />
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116 <conditional name="information">
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117 <param name="type" value="sequences" />
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118 <param name="to_download" value="PredictedCDSWithAnnotation" />
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119 </conditional>
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120 <output name="output_file_fasta">
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121 <assert_contents>
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122 <has_line_matching expression="^>ERR675573.1772-FC81EB0ABXX:7:1101:19215:2564-ATCACGAT-1_1_117_- IPR010690/PF06898/2-34$" />
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123 <has_line_matching expression="^>ERR675573.6692248-FC81EB0ABXX:7:1202:20007:191300-ATCACGAT-1_1_127_- IPR004089/PF00015/2-41|G3DSA:1.10.287.950/2-41$" />
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124 <has_line_matching expression="^>ERR675573.21754698-FC81EB0ABXX:7:2208:13328:189792-ATCACGAT-1_1_150_- IPR027414/G3DSA:2.70.98.50/7-45$" />
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125 </assert_contents>
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126 </output>
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127 </test>
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128 </tests>
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129
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130 <help><![CDATA[
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131 **What it does**
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132
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133 The European Bioinformatics Institute (EMBL-EBI) maintains the world’s most comprehensive range of freely available and up-to-date molecular databases
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134
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135 This tool download data related to a run in EBI Metagenomics database.
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136 ]]></help>
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137
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138 <expand macro="citations" />
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139 </tool>