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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
author | iuc |
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date | Sat, 21 Jan 2017 14:40:54 -0500 |
parents | e2e9fae080ad |
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<tool id="ebi_metagenomics_run_downloader" name="Download run data" version="0.1.0"> <description>from EBI Metagenomics database</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="7.49.0">curl</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ '$__tool_directory__/download_ebi_metagenomics_run_data' '$__tool_directory__/ebeye_urllib.py' '$run_id' '$information.type' '$information.to_download' #if ( $information.type == 'sequences' and $information.to_download != 'ncRNA-tRNA-FASTA') or ($information.type == 'function' and $information.to_download == 'InterProScan') 'multiple_chunks' #else 'single_chunk' #end if 'output.dat' ]]></command> <inputs> <param name="run_id" type="text" label="Identifiant of the run in EBI Metagenomics" /> <conditional name="information"> <param name="type" type="select" label="Type of information to download"> <option value="sequences" selected="true">Sequence data</option> <option value="qc-stats">Quality control statistics</option> <option value="taxonomy">Taxonomic analysis</option> <option value="function">Functional analysis</option> </param> <when value="sequences"> <param name="to_download" type="select" label="Sequences to download"> <option value="ProcessedReads" selected="true">Processed nucleotide reads</option> <option value="ReadsWithPredictedCDS">Processed reads with pCDS</option> <option value="ReadsWithMatches">Processed reads with annotation</option> <option value="ReadsWithoutMatches">Processed reads without annotation</option> <option value="PredictedCDSWithAnnotation">Predicted CDS with annotation</option> <option value="PredictedCDSWithoutAnnotation">Predicted CDS without annotation</option> <option value="PredictedORFWithoutAnnotation">Predicted ORF without annotation</option> <option value="ncRNA-tRNA-FASTA">Predicted tRNAs</option> </param> </when> <when value="qc-stats"> <param name="to_download" type="select" label="Quality control statistics to download"> <option value="summary" selected="true">Number of sequence reads per Quality Control step</option> <option value="stats">Quality control statistics</option> <option value="length">Read length distribution</option> <option value="gc_bin">Read GC distribution</option> <option value="base">Nucleotide position distribution</option> </param> </when> <when value="taxonomy"> <param name="to_download" type="select" label="Taxonomic analysis to download"> <option value="5S-rRNA-FASTA" selected="true">Reads encoding 5S rRNA</option> <option value="16S-rRNA-FASTA">Reads encoding 16S rRNA</option> <option value="23S-rRNA-FASTA">Reads encoding 23S rRNA</option> <option value="OTU-TSV">OTUs, reads and taxonomic assignments (TSV)</option> <option value="NewickPrunedTree">Phylogenetic tree</option> </param> </when> <when value="function"> <param name="to_download" type="select" label="Functional analysis to download"> <option value="InterProScan" selected="true">InterPro matches</option> <option value="GOAnnotations">Complete GO annotation</option> <option value="GOSlimAnnotations">GO slim annotation</option> </param> </when> </conditional> </inputs> <outputs> <data name="output_file_fasta" format="fasta" label="${tool.name} for ${run_id}" from_work_dir="output.dat"> <filter>( information['type'] == 'sequences' or ( information['type'] == 'taxonomy' and ( information['to_download'] == '5S-rRNA-FASTA' or information['to_download'] == '16S-rRNA-FASTA' or information['to_download'] == '23S-rRNA-FASTA' ))) </filter> </data> <data name="output_file_tsv" format="tsv" label="${tool.name} for ${run_id}" from_work_dir="output.dat"> <filter>( information['type'] == 'qc-stats' or ( information['type'] == 'taxonomy' and information['to_download'] == 'OTU-TSV' ) or ( information['type'] == 'function' and information['to_download'] == 'InterProScan/chunks/1' )) </filter> </data> <data name="output_file_csv" format="csv" label="${tool.name} for ${run_id}" from_work_dir="output.dat"> <filter>( information['type'] == 'function' and ( information['to_download'] == 'GOAnnotations' or information['to_download'] == 'GOSlimAnnotations' )) </filter> </data> <data name="output_file_newick" format="newick" label="${tool.name} for ${run_id}" from_work_dir="output.dat"> <filter>( information['type'] == 'taxonomy' and information['to_download'] == 'NewickPrunedTree') </filter> </data> </outputs> <tests> <test> <param name="run_id" value="ERR675640" /> <conditional name="information"> <param name="type" value="qc-stats" /> <param name="to_download" value="stats" /> </conditional> <output name="output_file_tsv" file="ERR675640_qc-stats_stats" /> </test> <test> <param name="run_id" value="ERR675573" /> <conditional name="information"> <param name="type" value="sequences" /> <param name="to_download" value="PredictedCDSWithAnnotation" /> </conditional> <output name="output_file_fasta"> <assert_contents> <has_line_matching expression="^>ERR675573.1772-FC81EB0ABXX:7:1101:19215:2564-ATCACGAT-1_1_117_- IPR010690/PF06898/2-34$" /> <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$" /> <has_line_matching expression="^>ERR675573.21754698-FC81EB0ABXX:7:2208:13328:189792-ATCACGAT-1_1_150_- IPR027414/G3DSA:2.70.98.50/7-45$" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ **What it does** The European Bioinformatics Institute (EMBL-EBI) maintains the world’s most comprehensive range of freely available and up-to-date molecular databases This tool download data related to a run in EBI Metagenomics database. ]]></help> <expand macro="citations" /> </tool>