diff humann2_renorm_table.xml @ 11:e504cd2410a6 draft

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

--- a/humann2_renorm_table.xml	Tue Apr 12 03:06:03 2016 -0400
+++ b/humann2_renorm_table.xml	Thu May 26 10:18:02 2016 -0400
@@ -1,5 +1,5 @@
-<tool id="humann2_renorm_table" name="Renormalize HUMAnN2 table" version="0.5.0">
-    <description></description>
+<tool id="humann2_renorm_table" name="Renormalize" version="0.6.1">
+    <description>a HUMAnN2 generated table</description>
 
     <macros>
         <import>humann2_macros.xml</import>
@@ -22,8 +22,7 @@
     ]]></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="norm" type="select" label="Normalization scheme" help="(--norm)">
             <option value="cpm" selected="true">Copies per million</option>
@@ -32,32 +31,30 @@
     </inputs>
 
     <outputs>
-        <data format="tsv" name="output_table" label="Normalized table for 
-            ${on_string} (HUMAnN2)" />
+        <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Normalized table" />
     </outputs>
 
     <tests>
         <test>
-            <param name="input_table" value="humann2_fasta_pathabundance.tsv"/>
+            <param name="input_table" value="expected_pathway_abundance.tsv"/>
             <param name="norm" value="cpm"/>
-            <output name="output_table" file="humann2_fasta_pathabundance_cpm_renormalized.tsv"/>
+            <output name="output_table" file="cpm_renormalized_pathway_abundance.tsv"/>
         </test>
         <test>
-            <param name="input_table" value="humann2_fasta_pathabundance.tsv"/>
+            <param name="input_table" value="expected_pathway_abundance.tsv"/>
             <param name="norm" value="relab"/>
-            <output name="output_table" file="humann2_fasta_pathabundance_relab_renormalized.tsv"/>
+            <output name="output_table" file="relab_renormalized_pathway_abundance.tsv"/>
         </test>
     </tests>
 
     <help><![CDATA[
-        **What it does**
+**What it does**
 
-        Renorm HUMAnN2 table is a tool for renormalizing table. Each level of a stratified table will be normalized using the desired scheme.
+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>`_.
+Renorm HUMAnN2 table is a tool to renormalize a table, either in copies per million or in relative abundance. Each level of a stratified table will be normalized using the desired scheme.
 
     ]]></help>
 
-    <citations>
-    </citations>
+    <expand macro="citations"/>
 </tool>
\ No newline at end of file