Mercurial > repos > iuc > humann_join_tables
view humann_infer_taxonomy @ 3:6c3271894a95 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 32d4c566afe55179531fdd106dc5a996cc09bbb1
author | iuc |
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date | Wed, 29 Mar 2023 20:02:22 +0000 |
parents | cf7f80d59099 |
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<!-- The tool is broken with current version of HUMAnN. Once it will be fixed, we can update this wrapper and add the XML extension to enable it --> <tool id="humann_infer_taxonomy" name="Infex taxonomy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>for "unclassified" taxonomy in HUMAnN generated gene families</description> <macros> <import>macros.xml</import> </macros> <expand macro="edam_ontology"/> <expand macro="requirements"/> <expand macro="version"/> <command detect_errors="exit_code"><![CDATA[ humann_infer_taxonomy --input '$input' --output '$output' --level '$level' --database '$database.fields.path' --mode '$mode' --lca-choice '$lca_choice' --threshold $threshold ]]></command> <inputs> <param argument="--input" type="data" format="tsv,tabular" label="Gene family table"/> <param argument="--level" type="select" label="Desired level for taxonomic estimation/summation"> <option value="Kingdom">Kingdom</option> <option value="Phylum">Phylum</option> <option value="Class">Class</option> <option value="Order">Order</option> <option value="Family" selected="true">Family</option> <option value="Genus">Genus</option> </param> <param argument="--database" type="select" label="UniRef-specific taxonomy database"> <options from_data_table="humann_utility_mapping"> <validator message="No utility mapping is available" type="no_options" /> <filter type="regexp" column="2" value="tol-lca" /> </options> </param> <param argument="--mode" type="select" label="Rows to include in the estimation/summation"> <option value="c_tmode" selected="true">Totals</option> <option value="c_umode">Unclassified</option> <option value="c_smode">Stratified</option> </param> <param argument="--lca-choice" type="select" label="Per-gene taxonomic annotation to consider"> <option value="source_tax">Source taxonomy</option> <option value="uniref_lca">UniRef lowest common ancestor (LCA)</option> <option value="humann_lca" selected="true">HUMAnN lowest common ancestor (LCA)</option> </param> <param argument="--threshold" type="float" value="1e-3" label="Minimum frequency for a new taxon to be included"/> </inputs> <outputs> <data format="tabular" name="output"/> </outputs> <tests> <test expect_num_outputs="1"> <param name="input" value=""/> <param name="level" value="Kingdom"/> <param name="database" value=""/> <param name="mode" value="c_tmode"/> <param name="lca_choice" value="source_tax"/> <param name="threshold" value="1e-3"/> <output name="output" ftype="tabular"> <assert_contents> <has_text text=""/> <has_line line=""/> <has_line_matching expression=""/> <has_n_columns n=""/> <has_size value="" delta=""/> </assert_contents> </output> </test> </tests> <help><![CDATA[ @HELP_HEADER@ Based on the lowest common ancestor (LCA) annotation of each UniRef50/90 cluster, this tool infers approximate taxonomy for unclassified features at a target level of resolution. It will modify features of known genus/species to match target level. ]]></help> <expand macro="citations"/> </tool>