Mercurial > repos > iuc > humann_reduce_table
diff humann_reduce_table.xml @ 0:c2488dbc8e39 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
author | iuc |
---|---|
date | Wed, 12 May 2021 09:00:46 +0000 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/humann_reduce_table.xml Wed May 12 09:00:46 2021 +0000 @@ -0,0 +1,53 @@ +<tool id="humann_reduce_table" name="Reduce" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>a joined HUMAnN table</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edam_ontology"/> + <expand macro="requirements"/> + <expand macro="version"/> + <command detect_errors="exit_code"><![CDATA[ +humann_reduce_table + --input '$input' + -o '$output' + --function '$function' + --sort-by '$sort_by' + ]]></command> + <inputs> + <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway/taxonomic table"/> + <param argument="--function" type="select" label="Function to apply to select value to keep"> + <option value="max" selected="true">Max</option> + <option value="sum">Sum</option> + <option value="mean">Mean</option> + <option value="min">Min</option> + </param> + <param argument="--sort-by" type="select" label="How to sort the output"> + <option value="name" selected="true">Name</option> + <option value="value">Value</option> + <option value="level">Level</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="output"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input" value="demo_joined_pathabundance_pathcoverage.tsv"/> + <param name="function" value="max"/> + <param name="sort_by" value="name"/> + <output name="output" ftype="tabular"> + <assert_contents> + <has_text text="max" /> + <has_text text="UNINTEGRATED|unclassified" /> + <has_text text="PWY-4203: volatile benzenoid biosynthesis I (ester formation)|unclassified" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +@HELP_HEADER@ + +This tool reduces a joined HUMAnN table. It selects for each row which value to keep given a function (max, sum, mean or min). + ]]></help> + <expand macro="citations"/> +</tool>