diff text-from-interval.xml @ 2:014a21767ac4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/text-from-interval.xml	Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,59 @@
+<?xml version="1.0"?>
+<tool id="circos_interval_to_text" name="Circos: Interval to Circos Text Labels" version="@WRAPPER_VERSION@">
+    <description>reformats interval files to prepare for Circos text labels</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+    </expand>
+    <command detect_errors="exit_code"><![CDATA[
+python
+#if $ref.ref_source == 'gff3':
+    '$__tool_directory__/text-from-gff3.py' '$input' '${ref.attr}'
+#else
+    '$__tool_directory__/text-from-bed.py' '$input'
+#end if
+> '$output'
+    ]]></command>
+    <inputs>
+        <conditional name="ref">
+            <param name="ref_source" type="select" label="Data Format">
+                <option value="bed" selected="true">BED6+</option>
+                <option value="gff3">GFF3</option>
+            </param>
+            <when value="bed">
+                <param name="input" type="data" format="bed" label="BED File (BED6+ only)" />
+            </when>
+            <when value="gff3">
+                <param name="input" type="data" format="gff3" label="GFF3 File" />
+                <param name="attr" type="text" label="GFF3 Attribute to pull value from" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="ref">
+                <param name="ref_source" value="bed" />
+                <param name="input" value="text/1.bed" ftype="bed" />
+            </conditional>
+            <output name="output" file="text/1.out" ftype="tabular" />
+        </test>
+        <test>
+            <conditional name="ref">
+                <param name="ref_source" value="gff3" />
+                <param name="input" value="text/2.gff3" ftype="gff3" />
+                <param name="attr" value="Name" />
+            </conditional>
+            <output name="output" file="text/2.out" ftype="tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Converts standard BED6+ and GFF3 files into a format appropriate for Circos data tracks, especially text tracks.
+
+BED3 files cannot be used as they lack the name field.
+    ]]></help>
+    <expand macro="citations" />
+</tool>