Mercurial > repos > iuc > biom_normalize_table

diff biom_normalize_table.xml @ 0:a900ebd4a533 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f609ae13de8441b0311e4817aca4f1d1635da028
author iuc
date Wed, 31 May 2017 11:20:30 -0400
parents
children ea1936aa2d98
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/biom_normalize_table.xml	Wed May 31 11:20:30 2017 -0400
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+<tool id="biom_normalize_table" name="Normalize" version="@VERSION@.1">
+    <description>a BIOM table</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code">
+        <![CDATA[
+            biom normalize-table
+              --input-fp '$input_fp'
+              --output-fp '$output_fp'
+              $relative_abund
+              $presence_absence
+              --axis '$axis'
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="BIOM table to normalize" />
+        <param name="relative_abund" argument="--relative-abund" type="boolean" checked="True" truevalue="--relative-abund" falsevalue="" label="Convert table to relative abundance" />
+        <param name="presence_absence" argument="--presence-absence" type="boolean" checked="True" truevalue="--presence-absence" falsevalue="" label="Convert table to presence/absence" />
+        <param argument="--axis" type="select" label="The axis to normalize over">
+            <option value="sample" selected="True">Sample</option>
+            <option value="observation">Observation</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="biom1" name="output_fp"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_fp" value="input_abundance_1.biom1" />
+            <param name="relative_abund" value="--relative-abund" />
+            <param name="presence_absence" value="" />
+            <param name="axis" value="sample" />
+            <output name="output_fp" value="normalized_relative_abund_samples.biom" ftype="biom1" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="input_fp" value="input_abundance_1.biom1" />
+            <param name="relative_abund" value="" />
+            <param name="presence_absence" value="--presence-absence" />
+            <param name="axis" value="observation" />
+            <output name="output_fp" value="normalized_presence_absence_observations.biom" ftype="biom1" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Normalize the values of a BIOM table through various methods. Relative abundance will take the relative abundance of each observation in terms of samples or observations.  Presence absensece will convert observations to 1's and 0's based on presence of the observation.
+    ]]></help>
+    <expand macro="citations" />
+</tool>