Mercurial > repos > iuc > hyphy_strike_ambigs

diff hyphy_strike_ambigs.xml @ 0:7c86ceaf523c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author iuc
date Tue, 20 Apr 2021 10:27:46 +0000
parents
children dc8875a13914
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_strike_ambigs.xml	Tue Apr 20 10:27:46 2021 +0000
@@ -0,0 +1,40 @@
+<?xml version="1.0"?>
+<tool id="hyphy_strike_ambigs" name="Replace ambiguous codons" version="@VERSION@">
+    <description>in a multiple alignment using HyPhy</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        hyphy '$__tool_directory__/scripts/strike-ambigs.bf'
+            --alignment '$alignment' --output '$output'
+        @ERRORS@
+        ]]></command>
+    <inputs>
+        <param name="alignment" type="data" format="fasta" label="Input alignment" />
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="alignment" ftype="fasta" value="strike-ambigs-in1.fa"/>
+            <output name="output" file="strike-ambigs-out1.fa" />
+        </test>
+        <test>
+            <param name="alignment" ftype="fasta" value="strike-ambigs-in2.fa"/>
+            <output name="output" file="strike-ambigs-out2.fa" />
+        </test>
+    </tests>
+    <help><![CDATA[
+HyPhy Strike-Ambigs
+===================
+
+Reads an alignment of coding sequences and replaces any ambiguous codons with ---.
+
+Note: The input fasta must be aligned along codon boundaries.
+]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1093/bioinformatics/bti079</citation>
+    </expand>
+</tool>