Mercurial > repos > mvdbeek > damidseq_consecutive_peaks

diff consecutive_peaks.xml @ 0:7ca388514216 draft

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planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
author mvdbeek
date Fri, 26 Oct 2018 11:56:10 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/consecutive_peaks.xml	Fri Oct 26 11:56:10 2018 -0400
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+<tool id="consecutive_peaks" name="Consecutive peaks" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="7.0">click</requirement>
+        <requirement type="package" version="0.23.4">pandas</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/consecutive_peaks.py' '$input_file' '$output_file'
+    ]]></command>
+    <inputs>
+       <param name="input_file" type="data" format="tabular" label="Input file" help="file containing peaks and genes"/>
+       <param name="padj_column" type="data_column" data_ref="input_file" value="c8" label="Column containing padj value"/>
+       <param name="groupby" type="data_column" data_ref="input_file" value="c9" label="Group values by this column" help="Usually gene id."/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format_source="input_file"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="deseq2_peaks.bed"/>
+            <output name="output_file" value="grouped.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Can be used to get the lowest p.adj for 2 consecutive peaks in a gene.
+The reported p.adj is the higher p.adj of the 2 consecutive peaks.
+    ]]></help>
+</tool>