diff glimmer_acgt_content.xml @ 0:4c74f770979d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glimmer_acgt_content.xml	Tue Nov 28 10:08:46 2017 -0500
@@ -0,0 +1,50 @@
+<tool id="glimmer_acgt_content" name="ACGT Content" version="@WRAPPER_VERSION@">
+    <description>of windows in each sequence</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command><![CDATA[
+        window-acgt
+            $percentage
+            $input_win_len
+            $input_win_skip
+            < '$infile' > '$output'
+
+            ##TODO prettify the output
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="fasta" label="Genome Sequence"/>
+        <param name="input_win_len" type="integer" value="10" label="The width of the sliding window"/>
+        <param name="input_win_skip" type="integer" value="10" label="The number of positions between windows to report"/>
+        <param name="percentage" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Report percentages instead of counts"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="streptomyces_Tu6071_genomic.fasta" />
+            <output name="output" file="streptomyces_Tu6071_genomic.acgt" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+**What it does**
+
+This tool calculates the ACGT-Content from a given Sequence, given a sliding window.
+
+-------
+
+**Output**
+
+Output is in the format:
+
+	window-start	window-len	A's	C's	G's	T's	#other	%GC
+
+Note the last window in the sequence can be shorter than *window-len* if the sequence ends prematurely
+]]>
+    </help>
+    <expand macro="citation" />
+</tool>