diff normalize_by_copynumber.xml @ 0:6273e2721fa3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/normalize_by_copynumber.xml	Thu Dec 08 06:28:17 2016 -0500
@@ -0,0 +1,61 @@
+<tool id="picrust_normalize_by_copy_number" name="Normalize" version="@WRAPPER_VERSION@.0">
+    <description>OTUs by copy number</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        normalize_by_copy_number.py
+            -i '$input_data'
+            -o tempbiom
+            -c '$gg.precalc'
+
+            @OUTPUT_CONVERSION_COMMANDS@
+    ]]></command>
+    <inputs>
+        <param name="input_data" type="data" format="tabular,biom1" label="Input file" help="biom file or legacy QIIME OTU table"/>
+        <expand macro="otu-reference-precalculated"/>
+        <expand macro="biom_format_select"/>
+    </inputs>
+    <outputs>
+        <expand macro="biom_output"/>
+    </outputs>
+    <tests>
+        <test> <!-- test with biom input -->
+            <param name="input_data" value="closed_picked_otus.biom"/>
+            <param name="source" value="hist"/>
+            <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
+            <param name="output_type" value="json"/>
+            <output name="out_biom" ftype="json">
+                <assert_contents>
+                    <has_text text="Biological Observation Matrix"/>
+                    <has_text text="generated_by"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test> <!-- test with QIIME input and classic output -->
+            <param name="input_data" value="closed_picked_otus.tab"/>
+            <param name="source" value="hist"/>
+            <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
+            <param name="output_type" value="tsv"/>
+            <output name="out_biom" file="normalized_otus.classic" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+@PICRUST_OVERVIEW@
+
+**Command Documenation**
+
+This module corrects the abundance of each OTU to better reflect the true organism abundance by normalizing by PICRUSt's prediction of 16S copy number for each OTU.
+
+Please ensure that you have properly created your OTU table to be compatible with PICRUSt by following this guide_.
+A sample file can be downloaded here_
+
+.. _guide: http://picrust.github.com/picrust/methods/constructing_reference_otus.html
+.. _here: https://raw.github.com/picrust/picrust/master/tutorials/hmp_mock_16S.tab
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>