diff artic_margin_cons_medaka.xml @ 0:7df876ad836a draft

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/artic_margin_cons_medaka.xml	Wed Mar 11 01:58:44 2020 +0000
@@ -0,0 +1,34 @@
+<tool id="artic_margin_cons_medaka" name="ARTIC margin_cons_medaka" version="0.1.0+galaxy0">
+    <description>Generate consensus fasta file from a reference fasta, bam alignment and VCF file</description>
+    <requirements>
+        <requirement type="package" version="0.6.8">pyvcf</requirement>
+        <requirement type="package" version="1.76">biopython</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '${__tool_directory__}/margin_cons_medaka.py'
+          --depth '${minimum_depth}'
+          --quality '${minimum_quality}'
+          '${ref_fasta}'
+          '${input_variants}'
+          '${input_alignment}'
+          > '${consensus_fasta}'
+          2> '${report}'
+    ]]></command>
+    <inputs>
+        <param name="ref_fasta" type="data" format="fasta" label="Reference Sequence"/>
+        <param name="input_alignment" type="data" format="bam" label="Input Alignment"/>
+        <param name="input_variants" type="data" format="vcf" label="Input Variants"/>
+        <param name="minimum_depth" type="int" value="5" min="1" max="500" label="Minimum depth to call a variant"/>
+        <param name="minimum_quality" type="int" value="0" min="0" max="100" label="Minimum quality to call a variant"/>
+    </inputs>
+    <outputs>
+        <data name="consensus_fasta" format="fasta" label="${tool.name} on ${on_string}: Consensus (.fasta)" />
+        <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+    ]]></help>
+    <citations>
+    </citations>
+</tool>