diff gc_skew.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/gc_skew.xml	Tue Sep 17 16:54:57 2019 -0400
@@ -0,0 +1,63 @@
+<?xml version="1.0"?>
+<tool id="circos_gc_skew" name="GC Skew" version="@WRAPPER_VERSION@">
+    <description>calculates skew over genomic sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+    </expand>
+    <command detect_errors="exit_code"><![CDATA[
+ln -s -f
+#if $reference_genome.reference_genome_source == "history"
+    '$reference_genome.history_item'
+#else
+    '$reference_genome.builtin.fields.path'
+#end if
+reference.fa &&
+
+python '$__tool_directory__/gc_skew.py' reference.fa '$window' '$output'
+    ]]></command>
+    <inputs>
+      <conditional name="reference_genome">
+        <param label="Source for reference genome" name="reference_genome_source" type="select">
+          <option selected="True" value="history">Use a genome from history</option>
+          <option value="builtin">Use a built-in genome"</option>
+        </param>
+        <when value="history">
+          <param format="fasta" type="data" name="history_item" label="Select a reference genome"/>
+        </when>
+        <when value="builtin">
+          <param label="Select a reference genome" name="builtin" type="select">
+            <options from_data_table="all_fasta">
+              <filter column="2" type="sort_by" />
+              <validator message="No genomes are available for the selected input dataset" type="no_options" />
+            </options>
+          </param>
+        </when>
+      </conditional>
+      <param argument="window" type="integer" min="1" value="100000" label="Window size" />
+    </inputs>
+    <outputs>
+      <data name="output" format="bigwig" />
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="reference_genome">
+                <param name="reference_genome_source" value="history" />
+                <param name="history_item" value="gc_skew/1.fa" ftype="fasta"/>
+            </conditional>
+            <param name="window" value="2" />
+            <output name="output" file="gc_skew/1.bw" ftype="bigwig" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Calculate GC skew (G-C)/(G+C) for multiple windows along the sequence.
+
+Returns a list of ratios (floats), controlled by the length of the sequence and the size of the window.
+
+Returns 0 for windows without any G/C by handling zero division errors.
+
+Does NOT look at any ambiguous nucleotides.
+    ]]></help>
+    <expand macro="citations" />
+</tool>