Mercurial > repos > mvdbeek > damid_deseq2_to_peaks

diff damid_deseq2_to_peaks.xml @ 0:3fd7995da4fd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
author mvdbeek
date Mon, 07 Jan 2019 12:58:55 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/damid_deseq2_to_peaks.xml	Mon Jan 07 12:58:55 2019 -0500
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+<tool id="damid_deseq2_to_peaks" name="DamID deseq2 to peaks" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="7">click</requirement>
+        <requirement type="package" version="0.23.4">pandas</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/damid_deseq2_to_peaks.py' '$input' '$output' --p_value_cutoff $p_value_cutoff
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Select DESeq2 result file for GATC sites"/>
+        <param argument="p_value_cutoff" type="float" value="0.01" min="0" max="1" label="Select minimum p-value to consider a GATC significantly bound"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="bed"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="test_data.tab"/>
+            <output name="output" value="peaks.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Converts a deseq2 GATC result file into peaks in bed format.
+    ]]></help>
+</tool>