diff humann2_split_table.xml @ 0:8ed686bd4229 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_split_table.xml	Mon Mar 13 12:37:33 2017 -0400
@@ -0,0 +1,52 @@
+<tool id="humann2_split_table" name="Split" version="@WRAPPER_VERSION@.0">
+    <description> a HUMAnN2 generated table</description>
+    <macros>
+        <import>humann2_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+        humann2_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" label="${tool.name} on ${on_string}: Split tables">
+            <discover_datasets pattern="__designation_and_ext__" directory="output"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="joined_pathway_coverage_abundance.tsv"/>
+            <output_collection name="split_tables" type="list" >
+                <element name="demo_Coverage" file="demo_Coverage.tsv" />
+                <element name="demo_Abundance" file="demo_Abundance.tsv" />
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+Split HUMAnN2 table is a tool to split a gene table with multiple columns. This file can have been generated with the join table tool.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>