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
--- /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>