Mercurial > repos > public-health-bioinformatics > antigenic_site_extraction

diff antigenic_site_extraction.xml @ 0:a1b46e339580 draft default tip

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planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit b96b6e06f6eaa6ae8ef4c24630dbb72a4aed7dbe
author public-health-bioinformatics
date Thu, 04 Jul 2019 19:36:38 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/antigenic_site_extraction.xml	Thu Jul 04 19:36:38 2019 -0400
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+<tool id="antigenic_site_extraction" name="Antigenic Site Extraction" version="0.0.1">
+  <requirements>
+    <requirement type="package" version="1.70">biopython</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+    python $__tool_directory__/antigenic_site_extraction.py
+    '$input_fasta'
+    '$index_array'
+    '$output_file'
+    #if $csv
+    	-c
+    #end if
+  ]]></command>
+  <inputs>
+    <param name="input_fasta" format="fasta" type="data" />
+    <param name="index_array" format="csv" type="data" />
+    <param name="csv" type="boolean" label="Output to csv ?" />
+  </inputs>
+  <outputs>
+      <data format="fasta" name="output_file">
+        <change_format>
+            <when input="csv" value="true" format="csv" />
+        </change_format>
+      </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_fasta" value="14_H3_aa_seqs_aligned.fasta" />
+      <param name="index_array" value="FluA_H3_antigenic_aa_indices.csv" />
+      <output name="output_file" value="output.fasta" />
+    </test>
+  </tests>
+  <help><![CDATA[
+    Upload a fasta file containing full length flu sequences and an index array csv file.
+  ]]></help>
+  <citations>
+  </citations>
+</tool>