Mercurial > repos > czouaoui > abundance_table_to_biom1

changeset 2:613e054cad7f draft

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Uploaded
author czouaoui
date Tue, 20 Mar 2018 04:26:35 -0400
parents 10eedb4b587f
children ebd4a477b19e
files abundanceTable_to_biom.xml
diffstat 1 files changed, 22 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abundanceTable_to_biom.xml	Tue Mar 20 04:26:35 2018 -0400
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+<tool id="abundanceTable_to_biom" name="Converting abundance tables to Biom files (v1.0)" version="0.1.0">
+    <command detect_errors="exit_code"><![CDATA[
+        python $__tool_directory__/abundanceTable_to_biom.py --file $input --out_name biom_result
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" format="csv" label="Abundance table"/>
+    </inputs>
+    <outputs>
+        <data name= "output" format="biom1" label="${input.name} to Biom (v1.0)" from_work_dir="biom_result.biom"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" format="csv" value="merge_summary_reads.csv"/>
+            <output name="output" format="biom1" file="biom_result.biom"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool is used to generate a Biom file (v1.0) from an abundance table. 
+	The first column of the header is a taxonomy list (families). Next columns contain sample ids.
+	The abundancy of reads is set inside the table. 
+    ]]></help>
+</tool>