diff poretools_occupancy.xml @ 0:336791b5665f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/poretools_occupancy.xml	Tue Dec 19 14:47:30 2017 -0500
@@ -0,0 +1,51 @@
+<?xml version="1.0"?>
+<tool id="poretools_occupancy" name="Plot performance" version="@VERSION@.0">
+    <description>per cell in nanopore reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive">
+    <![CDATA[
+        poretools occupancy
+            '$input'
+            --saveas occupancy.$extension
+            --plot-type $plot_type
+        &&
+        mv occupancy.$extension '$output'
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
+        <param name="extension" type="select" label="File format for histogram">
+            <option value="png">PNG</option>
+            <option value="pdf">PDF</option>
+            <option value="svg">SVG</option>
+        </param>
+        <param name="plot_type" argument="--plot-type" type="select" label="Plot type to generate">
+            <option value="read_count">Read count</option>
+            <option value="total_bp">Total base pairs</option>
+        </param>
+    </inputs>
+    <outputs>
+        <expand macro="image_output" />
+    </outputs>
+    <tests>
+        <test>
+            <expand macro="test_input" />
+            <param name="extension" value="png" />
+            <param name="plot_type" value="read_count" />
+	    <output name="output" file="poretools-occupancy-out1.png" ftype="png" lines_diff="420" />
+        </test>
+        <test>
+            <expand macro="test_input" />
+            <param name="extension" value="pdf" />
+            <param name="plot_type" value="total_bp" />
+            <output name="output" file="poretools-occupancy-out1.pdf" ftype="pdf" lines_diff="36" />
+        </test>
+    </tests>
+    <help>
+        Plot the throughput performance of each pore on the flowcell during a given sequencing run.
+    </help>
+    <expand macro="citations" />
+</tool>