diff humann2_rename_table.xml @ 11:e504cd2410a6 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty

--- a/humann2_rename_table.xml	Tue Apr 12 03:06:03 2016 -0400
+++ b/humann2_rename_table.xml	Thu May 26 10:18:02 2016 -0400
@@ -1,5 +1,5 @@
-<tool id="humann2_rename_table" name="Rename HUMAnN2 table features" version="0.5.0">
-    <description></description>
+<tool id="humann2_rename_table" name="Rename" version="0.6.1">
+    <description>features of a HUMAnN2 generated table</description>
 
     <macros>
         <import>humann2_macros.xml</import>
@@ -19,45 +19,50 @@
             -i $input_table
             -o $output_table
 
-            --names $built_in.names
-            $built_in.simplify 
-            -c $built_in.file
+            --names $names
+            $simplify 
+
+            -c $mapping_file
     ]]></command>
 
     <inputs>
-        <param name="input_table" type="data" format="tsv" label="Gene/pathway 
-            table" help=""/>
+        <param name="input_table" type="data" format="tsv" label="Gene/pathway table" help="(-i)"/>
 
-        <param name="names" type="select" label="Table features that 
-        can be renamed" help="(--names)">
+        <param name="names" type="select" label="Table features that can be renamed" help="(--names)">
             <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
             <option value="metacyc-pwy">MetaCyc pathways</option>
             <option value="ko">KEGG Orthogroups (KO)</option>
             <option value="ec">Enzyme commision (EC)</option>
             <option value="uniref50">UniRef50 gene families</option>
         </param>
-        <param name='simplify' type='boolean' checked="false" truevalue='-s' 
-            falsevalue='' label="Remove non-alphanumeric characters from names?" 
-            help="(--simplify)"/>
-        <param name="file" type="data" format="tsv" label="Custom mapping file of feature IDs to full names" help="(--custom)"/>
+
+        <param name='simplify' type='boolean' checked="false" truevalue='-s' falsevalue='' label="Remove non-alphanumeric characters from names?" help="(--simplify)"/>
+
+        <param name="mapping_file" type="data" format="tsv" label="Mapping file" help="The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new value (--custom)"/>
+       
     </inputs>
 
     <outputs>
-        <data format="tsv" name="output_table" label="Renamed table for 
-            ${on_string} (HUMAnN2)" />
+        <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Renamed table" />
     </outputs>
 
     <tests>
+        <test>
+            <param name="input_table" value="expected_pathway_abundance.tsv"/>
+            <param name="names" value="metacyc-pwy" />
+            <param name='simplify' value=""/>
+            <param name="mapping_file" value="pathway_rename_mapping.tsv"/>
+            <output name="output_table" file="renamed_metacyc_pathways.tsv" />
+        </test>
     </tests>
 
     <help><![CDATA[
-        **What it does**
+**What it does**
 
-        Rename HUMAnN2 table features is a tool for renaming table features given built-in or custom mapping.
+HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
 
-        HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
+Rename HUMAnN2 table features is a tool for renaming table features given a custom mapping. The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new valu
     ]]></help>
 
-    <citations>
-    </citations>
+    <expand macro="citations"/>
 </tool>
\ No newline at end of file