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diff poretools_squiggle.xml @ 0:ce8af9373061 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
author iuc
date Tue, 19 Dec 2017 14:49:34 -0500
parents
children 34553d0caa5e
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/poretools_squiggle.xml	Tue Dec 19 14:49:34 2017 -0500
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+<?xml version="1.0"?>
+<tool id="poretools_squiggle" name="Plot signals" version="@VERSION@.0">
+    <description>for nanopore reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive">
+    <![CDATA[
+        poretools squiggle '$input' --saveas $extension --num-facets $num_facets
+            $theme_bw
+    ]]>
+    </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" />
+        <param name="num_facets" argument="--num-facets" type="integer" value="6" label="Number of plot facets" />
+    </inputs>
+    <outputs>
+        <data format="txt" name="output">
+            <discover_datasets pattern="__designation_and_ext__" directory="." visible="true" />
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <expand macro="test_input" />
+            <param name="extension" value="png" />
+            <output name="output">
+                <discovered_dataset designation="2016_3_4_3507_1_ch128_read430_strand.fast5" file="poretools-squiggle-out1-1.png" lines_diff="986" />
+                <discovered_dataset designation="2016_3_4_3507_1_ch128_read95_strand.fast5" file="poretools-squiggle-out1-2.png" lines_diff="883" />
+            </output>
+        </test>
+        <test>
+            <expand macro="test_input" />
+            <param name="extension" value="pdf" />
+            <output name="output">
+                <discovered_dataset designation="2016_3_4_3507_1_ch128_read430_strand.fast5" file="poretools-squiggle-out1-1.pdf" lines_diff="35" />
+                <discovered_dataset designation="2016_3_4_3507_1_ch128_read95_strand.fast5" file="poretools-squiggle-out1-2.pdf" lines_diff="35" />
+            </output>
+        </test>
+    </tests>
+    <help>
+        Plot the observed signals for FAST5 reads.
+    </help>
+    <expand macro="citations" />
+</tool>