diff hyphy_conv.xml @ 0:9ce3d6d4bd0e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hyphy_conv.xml	Tue Apr 20 10:31:50 2021 +0000
@@ -0,0 +1,47 @@
+<?xml version="1.0"?>
+<tool id="hyphy_conv" name="HyPhy-Conv" version="@VERSION@+galaxy0" profile="19.09">
+    <description>translate an in-frame codon alignment to proteins</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        cp '$input_file' conv_input.fa &&
+        hyphy conv
+            '$gencodeid'
+            '$deletions'
+            conv_input.fa
+            aa.nhx
+            > ./conv.log
+        @ERRORS@
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="fasta" label="Input codon alignment"/>
+        <param name="save_log" type="boolean" truevalue="Yes" falsevalue="No" checked="false" label="Save the conversion log to your history" />
+        <expand macro="gencode"/>
+        <param name="deletions" type="boolean" truevalue="Keep Deletions" falsevalue="Skip Deletions" label="Keep deletions" help="If this is checked, deletions will be left in the output file"/>
+    </inputs>
+    <outputs>
+        <data name="conv_log" format="txt" from_work_dir="conv.log">
+            <filter>save_log</filter>
+        </data>
+        <data name="proteins" format="nhx" from_work_dir="aa.nhx" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="fasta" value="conv-in1.fa"/>
+            <param name="deletions" value="Keep Deletions" />
+            <output name="proteins" file="conv-out1.nhx" />
+        </test>
+    </tests>
+    <help><![CDATA[
+HyPhy-CONV: Translate an in-frame codon alignment to proteins
+=============================================================
+
+This tool takes a codon-aligned fasta file and outputs the amino acid sequence
+it represents, with the option to keep or skip deletions in the input file.
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>
+