Mercurial > repos > iuc > humann2_renorm_table

diff humann2_renorm_table.xml @ 0:ba4dfbdc1295 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
author iuc
date Mon, 13 Mar 2017 12:38:56 -0400
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children dbf0e8eeeeed
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann2_renorm_table.xml	Mon Mar 13 12:38:56 2017 -0400
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+<tool id="humann2_renorm_table" name="Renormalize" 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_renorm_table
+            --input '$input'
+            -o '$output_table'
+            --units '$units'
+            --mode '$mode'
+            --special '$special'
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
+        <param argument="--units" type="select" label="Normalization scheme">
+            <option value="cpm" selected="true">Copies per million</option>
+            <option value="relab">Relative abundance</option>
+        </param>
+        <param argument="--mode" type="select" label="Normalization level">
+            <option value="community" selected="true">Normalization of all levels by community total</option>
+            <option value="levelwise">Normalization of all levels by levelwise total</option>
+        </param>
+        <param argument="--special" type='boolean' checked="true" truevalue='y' falsevalue='n' label="Include the special features UNMAPPED, UNINTEGRATED, and UNGROUPED?"/>
+    </inputs>
+    <outputs>
+        <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Normalized table" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="demo_pathabundance.tsv"/>
+            <param name="units" value="cpm"/>
+            <param name="mode" value="community"/>
+            <param name="special" value="n"/>
+            <output name="output_table" file="cpm_community_renormalized_pathway_abundance.tsv"/>
+        </test>
+        <test>
+            <param name="input" value="demo_pathabundance.tsv"/>
+            <param name="units" value="relab"/>
+            <param name="mode" value="levelwise"/>
+            <param name="special" value="y"/>
+            <output name="output_table" file="relab_levelwise_renormalized_pathway_abundance.tsv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+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>
+    <expand macro="citations"/>
+</tool>