diff poretools_qualpos.xml @ 0:2e22ebec211a 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_qualpos.xml	Tue Dec 19 14:53:26 2017 -0500
@@ -0,0 +1,45 @@
+<?xml version="1.0"?>
+<tool id="poretools_qualpos" name="Generate box-whisker" version="@VERSION@.0">
+    <description>plot of quality score distribution over positions in nanopore reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive">
+    <![CDATA[
+        poretools qualpos '$input' --saveas qualpos.$extension --min-length $min_length
+            --max-length $max_length --bin-width $bin_width $theme_bw && mv qualpos.$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" />
+        <expand macro="plot_options">
+            <option value="pdf">PDF</option>
+            <option value="svg">SVG</option>
+        </expand>
+        <param name="theme_bw" argument="--theme-bw" type="boolean" truevalue="--theme-bw" falsevalue="" label="Use a monochrome color " />
+        <expand macro="length_options" />
+        <param name="bin_width" argument="--bin-width" type="integer" value="1000" label="The width of bins" />
+    </inputs>
+    <outputs>
+        <expand macro="image_output">
+            <when input="extension" value="svg" format="svg" />
+        </expand>
+    </outputs>
+    <tests>
+        <test>
+            <expand macro="test_input" />
+            <param name="extension" value="png" />
+            <output name="output" file="poretools-qualpos-out1.png" ftype="png" lines_diff="195" />
+        </test>
+        <test>
+            <expand macro="test_input" />
+            <param name="extension" value="pdf" />
+            <output name="output" file="poretools-qualpos-out1.pdf" ftype="pdf" lines_diff="36" />
+        </test>
+    </tests>
+    <help>
+        Produce a box-whisker plot of quality score distribution over positions in nanopore reads
+    </help>
+    <expand macro="citations" />
+</tool>