annotate consecutive_peaks.xml @ 1:f3ca59e53b73 draft default tip

planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
author mvdbeek
date Mon, 29 Oct 2018 06:49:17 -0400
parents 7f827a8e4ec5
children
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7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents:
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1 <tool id="consecutive_peaks" name="Consecutive peaks" version="0.1.0">
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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2 <requirements>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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3 <requirement type="package" version="7.0">click</requirement>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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4 <requirement type="package" version="0.23.4">pandas</requirement>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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5 </requirements>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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6 <command detect_errors="exit_code"><![CDATA[
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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7 python '$__tool_directory__/consecutive_peaks.py' '$input_file' '$output_file'
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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8 ]]></command>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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9 <inputs>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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10 <param name="input_file" type="data" format="tabular" label="Input file" help="file containing peaks and genes"/>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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11 <param name="padj_column" type="data_column" data_ref="input_file" value="c8" label="Column containing padj value"/>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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12 <param name="groupby" type="data_column" data_ref="input_file" value="c9" label="Group values by this column" help="Usually gene id."/>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents:
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13 </inputs>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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14 <outputs>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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15 <data name="output_file" format_source="input_file"/>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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16 </outputs>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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17 <tests>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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18 <test>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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19 <param name="input_file" value="deseq2_peaks.bed"/>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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20 <output name="output_file" value="grouped.bed"/>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents:
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21 </test>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents:
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22 </tests>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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23 <help><![CDATA[
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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24 Can be used to get the lowest p.adj for 2 consecutive peaks in a gene.
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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25 The reported p.adj is the higher p.adj of the 2 consecutive peaks.
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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26 ]]></help>
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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27 </tool>