diff humann2_rename_table.xml @ 0:3d6f37e7e3a8 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_rename_table.xml	Thu May 26 10:20:59 2016 -0400
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+<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>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <version_command>
+<![CDATA[
+    humann2_rename_table --version
+]]>
+    </version_command>
+
+    <command><![CDATA[
+        humann2_rename_table
+            -i $input_table
+            -o $output_table
+
+            --names $names
+            $simplify 
+
+            -c $mapping_file
+    ]]></command>
+
+    <inputs>
+        <param name="input_table" type="data" format="tsv" label="Gene/pathway table" help="(-i)"/>
+
+        <param name="names" type="select" label="Table features that can be renamed" help="(--names)">
+            <option value="metacyc-rxn" selected="true">MetaCyc reactions</option>
+            <option value="metacyc-pwy">MetaCyc pathways</option>
+            <option value="ko">KEGG Orthogroups (KO)</option>
+            <option value="ec">Enzyme commision (EC)</option>
+            <option value="uniref50">UniRef50 gene families</option>
+        </param>
+
+        <param name='simplify' type='boolean' checked="false" truevalue='-s' falsevalue='' label="Remove non-alphanumeric characters from names?" help="(--simplify)"/>
+
+        <param name="mapping_file" type="data" format="tsv" label="Mapping file" help="The mapping file must be tabular format file with two tab-separated columns. The first column must contain the value you want to modify and the second contain the new value (--custom)"/>
+       
+    </inputs>
+
+    <outputs>
+        <data format="tsv" name="output_table" label="${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**
+
+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>
+
+    <expand macro="citations"/>
+</tool>
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