Mercurial > repos > iuc > circos

diff alignments-to-links.xml @ 2:014a21767ac4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
author: iuc
date: Tue, 17 Sep 2019 16:54:57 -0400
children: df7356989ac1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignments-to-links.xml	Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,28 @@
+<?xml version="1.0"?>
+<tool id="circos_aln_to_links" name="Circos: Alignments to links" version="@WRAPPER_VERSION@">
+    <description>reformats alignment files to prepare for Circos</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+    </expand>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/alignments-to-links.py' '$input' '$input.ext' > '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="maf,xmfa,stockholm" label="Alignment file (maf, xmfa, stockholm)" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="alignments/1.maf" ftype="maf" />
+            <output name="output" file="alignments/1.tab" ftype="tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Converts several standard alignment formats into a format appropriate for Circos plots.
+    ]]></help>
+    <expand macro="citations" />
+</tool>