Mercurial > repos > mvdbeek > damid_deseq2_to_peaks

annotate damid_deseq2_to_peaks.xml @ 0:3fd7995da4fd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
1 <tool id="damid_deseq2_to_peaks" name="DamID deseq2 to peaks" version="0.1.0">
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
2 <requirements>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
3 <requirement type="package" version="7">click</requirement>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
4 <requirement type="package" version="0.23.4">pandas</requirement>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
5 </requirements>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
7 python '$__tool_directory__/damid_deseq2_to_peaks.py' '$input' '$output' --p_value_cutoff $p_value_cutoff
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
8 ]]></command>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
9 <inputs>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
10 <param name="input" type="data" format="tabular" label="Select DESeq2 result file for GATC sites"/>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
11 <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"/>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
12 </inputs>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
13 <outputs>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
14 <data name="output" format="bed"/>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
15 </outputs>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
16 <tests>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
17 <test>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
18 <param name="input" value="test_data.tab"/>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
19 <output name="output" value="peaks.bed"/>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
20 </test>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
21 </tests>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
22 <help><![CDATA[
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
23 Converts a deseq2 GATC result file into peaks in bed format.
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
24 ]]></help>
3fd7995da4fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_peaks commit f37f4b741fd81f663d10523e1636039578c5bb55
mvdbeek
parents:
diff changeset
25 </tool>