Mercurial > repos > iuc > cat_contigs
view cat_contigs.xml @ 0:11a61934bfb3 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
author | iuc |
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date | Tue, 10 Dec 2019 16:05:34 -0500 |
parents | |
children | c6c77d840993 |
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<tool id="cat_contigs" name="CAT contigs" version="@VERSION@.0"> <description>annotate with taxonomic classification</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ CAT contigs -c '$contigs_fasta' @CAT_DB@ @USE_INTERMEDIATES@ @CUSTOM_SETTINGS@ @DIAMOND_OPTIONS@ && @TXT2TSV@ *.ORF2LCA.txt *.contig2classification.txt @ADD_NAMES@ @SUMMARISE@ ]]></command> <inputs> <param name="contigs_fasta" type="data" format="fasta" label="Contigs fasta"/> <expand macro="cat_db" /> <expand macro="use_intermediates" /> <expand macro="custom_settings" /> <expand macro="diamond_options" /> <expand macro="add_names" /> <expand macro="summarise" /> <expand macro="select_cat_outputs" /> </inputs> <outputs> <expand macro="outputs" /> </outputs> <tests> <test> <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/> <expand macro="test_catdb"/> <param name="select_outputs" value="contig2classification"/> <output name="contig2classification"> <assert_contents> <has_text text="contig_38063" /> </assert_contents> </output> </test> <test> <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/> <expand macro="test_catdb"/> <param name="select_outputs" value="predicted_proteins_faa"/> <conditional name="names"> <param name="add_names" value="both"/> </conditional> <param name="summarise" value="classification"/> <output name="predicted_proteins_faa"> <assert_contents> <has_text text=">contig_9952" /> </assert_contents> </output> <output name="orf2lca_names"> <assert_contents> <has_text text="Listeria" /> </assert_contents> </output> <output name="classification_summary"> <assert_contents> <has_text text="Listeria" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ **CAT contigs** Classifiy metagenomics contigs. @COMMON_HELP@ @OUTPUTS_HELP@ **CAT contigs** Run Contig Annotation Tool (CAT). Required arguments: -c, --contigs_fasta Path to contigs fasta file. -d, --database_folder Path to folder that contains database files. -t, --taxonomy_folder Path to folder that contains taxonomy files. @OPTIONS_HELP@ ]]></help> <expand macro="citations" /> </tool>