Mercurial > repos > mvdbeek > damidseq_consecutive_peaks

comparison consecutive_peaks.xml @ 0:7f827a8e4ec5 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 11:58:06 -0400
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1 <tool id="consecutive_peaks" name="Consecutive peaks" version="0.1.0">
2 <requirements>
3 <requirement type="package" version="7.0">click</requirement>
4 <requirement type="package" version="0.23.4">pandas</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/consecutive_peaks.py' '$input_file' '$output_file'
8 ]]></command>
9 <inputs>
10 <param name="input_file" type="data" format="tabular" label="Input file" help="file containing peaks and genes"/>
11 <param name="padj_column" type="data_column" data_ref="input_file" value="c8" label="Column containing padj value"/>
12 <param name="groupby" type="data_column" data_ref="input_file" value="c9" label="Group values by this column" help="Usually gene id."/>
13 </inputs>
14 <outputs>
15 <data name="output_file" format_source="input_file"/>
16 </outputs>
17 <tests>
18 <test>
19 <param name="input_file" value="deseq2_peaks.bed"/>
20 <output name="output_file" value="grouped.bed"/>
21 </test>
22 </tests>
23 <help><![CDATA[
24 Can be used to get the lowest p.adj for 2 consecutive peaks in a gene.
25 The reported p.adj is the higher p.adj of the 2 consecutive peaks.
26 ]]></help>
27 </tool>