Mercurial > repos > public-health-bioinformatics > aggregate_linelisting

diff aggregate_linelisting.xml @ 0:515c0c885f5d 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 19:40:13 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aggregate_linelisting.xml	Thu Jul 04 19:40:13 2019 -0400
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+<tool id="aggregate_linelisting" name="Aggregate Line List" version="0.0.1">
+  <requirements>
+    <requirement type="package" version="1.70">biopython</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+    python $__tool_directory__/aggregate_linelisting.py
+    '$input_fasta'
+    '$ref_fasta'
+    '$index_array_csv'
+    '$clade_def_csv'
+    '$output_file'
+  ]]></command>
+  <inputs>
+    <param name="input_fasta" format="fasta" type="data" label="Sample Sequences fasta."/>
+    <param name="ref_fasta" format="fasta" type="data" label="Reference Sequence fasta."/>
+    <param name="index_array_csv" format="csv" type="data" label="Antigenic Site Index Array File."/>
+    <param name="clade_def_csv" format="csv" type="data" label="Clade Definition File."/>
+  </inputs>
+  <outputs>
+    <data name="output_file" format="csv"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_fasta" value="fluA_H3_clade_assigned_antigenic_sites_extracted.fasta"/>
+      <param name="ref_fasta" value="MAP_3C.2a_A_Hong_Kong_4801_2014_X-263B_EGG.fasta" />
+      <param name="index_array_csv" value="FluA_H3_antigenic_aa_indices.csv" />
+      <param name="clade_def_csv" value="Flu_Clade_Definitions_H3_20171121.csv" />
+      <output name="output_file" value="test_output.csv"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+  ]]></help>
+  <citations>
+  </citations>
+</tool>