diff humann_split_table.xml @ 0:40a24d7612b8 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 6b06711cfba45855d5a992ed1c73c472eaef644f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann_split_table.xml	Mon Feb 13 16:17:26 2023 +0000
@@ -0,0 +1,63 @@
+<tool id="humann_split_table" name="Split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
+    <description> a merged 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_split_table
+    --input '$input'
+    -o 'output'
+#if $taxonomy_index
+    --taxonomy_index '$taxonomy_index'
+#end if
+#if $taxonomy_level
+    --taxonomy_level '$taxonomy_level'
+#end if
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="tsv,tabular,biom1" label="Gene table to split"/>
+        <param argument="--taxonomy_index" type="text" label="Index of the gene in the taxonomy data" optional="true"/>
+        <param argument="--taxonomy_level" type="select" label="Level of taxonomy for the output" optional="true" help="If input is from picrust metagenome_contributions.py">
+            <option value="Kingdom">Kingdom</option>
+            <option value="Phylum">Phylum</option>
+            <option value="Class">Class</option>
+            <option value="Order">Order</option>
+            <option value="Family">Family</option>
+            <option value="Genus">Genus</option>
+            <option value="Species">Species</option>
+        </param>
+    </inputs>
+    <outputs>
+        <collection type="list" name="split_tables">
+            <discover_datasets pattern="__designation_and_ext__" directory="output"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="demo_joined_pathabundance_pathcoverage.tsv"/>
+            <output_collection name="split_tables" type="list">
+                <element name="humann_Abundance" ftype="tsv">
+                    <assert_contents>
+                        <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
+                        <has_n_columns n="2"/>
+                    </assert_contents>
+                </element>
+                <element name="humann_Coverage" ftype="tsv">
+                    <assert_contents>
+                        <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
+                        <has_n_columns n="2"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+This tool splits a merged feature table (multiple samples) into one file per sample. Some analyses can only accept one sample at a time.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>