diff humann2_renorm_table.xml @ 1:dbf0e8eeeeed draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee

--- a/humann2_renorm_table.xml	Mon Mar 13 12:38:56 2017 -0400
+++ b/humann2_renorm_table.xml	Tue Aug 01 07:55:54 2017 -0400
@@ -6,12 +6,13 @@
     <expand macro="requirements"/>
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
-        humann2_renorm_table
-            --input '$input'
-            -o '$output_table'
-            --units '$units'
-            --mode '$mode'
-            --special '$special'
+humann2_renorm_table
+    --input '$input'
+    -o '$output_table'
+    --units '$units'
+    --mode '$mode'
+    --special '$special'
+    $update_snames
     ]]></command>
     <inputs>
         <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
@@ -23,7 +24,8 @@
             <option value="community" selected="true">Normalization of all levels by community total</option>
             <option value="levelwise">Normalization of all levels by levelwise total</option>
         </param>
-        <param argument="--special" type='boolean' checked="true" truevalue='y' falsevalue='n' label="Include the special features UNMAPPED, UNINTEGRATED, and UNGROUPED?"/>
+        <param argument="--special" type='boolean' truevalue='y' falsevalue='n' checked="true" label="Include the special features UNMAPPED, UNINTEGRATED, and UNGROUPED?"/>
+        <param name="update_snames" argument="--update-snames" type='boolean' truevalue='--update-snames' falsevalue='' checked="true" label="Update '-RPK' in sample names to appropriate suffix?"/>
     </inputs>
     <outputs>
         <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Normalized table" />
@@ -34,6 +36,7 @@
             <param name="units" value="cpm"/>
             <param name="mode" value="community"/>
             <param name="special" value="n"/>
+            <param name="update_snames" value=""/>
             <output name="output_table" file="cpm_community_renormalized_pathway_abundance.tsv"/>
         </test>
         <test>
@@ -41,6 +44,7 @@
             <param name="units" value="relab"/>
             <param name="mode" value="levelwise"/>
             <param name="special" value="y"/>
+            <param name="update_snames" value=""/>
             <output name="output_table" file="relab_levelwise_renormalized_pathway_abundance.tsv"/>
         </test>
     </tests>