Mercurial > repos > mvdbeek > bam_readtagger
comparison filter_insertions.xml @ 39:432bb619c079 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
author | mvdbeek |
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date | Thu, 15 Mar 2018 07:20:58 -0400 |
parents | f6311a04a6c9 |
children | 4b1ebfcd0f46 |
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38:f6311a04a6c9 | 39:432bb619c079 |
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3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.4.9">readtagger</requirement> | 4 <requirement type="package" version="0.4.9">readtagger</requirement> |
5 </requirements> | 5 </requirements> |
6 <version_command>confirm_insertions --version</version_command> | 6 <version_command>confirm_insertions --version</version_command> |
7 <command detect_errors="aggressive"><![CDATA[ | 7 <command detect_errors="aggressive"><![CDATA[ |
8 ln -fs $putative_insertions putative_insertions.gff && | |
9 ln -fs $all_insertions all_insertions.gff && | |
10 ln -fs $all_controls all_controls_path.gff && | |
8 confirm_insertions | 11 confirm_insertions |
9 --putative_insertions_path '$putative_insertions' | 12 --putative_insertions_path putative_insertions.gff |
10 --all_treatments_path '$all_insertions' | 13 --all_treatments_path all_insertions.gff |
11 --all_controls_path '$all_controls' | 14 --all_controls_path all_controls_path.gff |
12 --output_path '$output' | 15 --output_path '$output' |
13 $output_discard | 16 $output_discard |
14 ]]></command> | 17 ]]></command> |
15 <inputs> | 18 <inputs> |
16 <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/> | 19 <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/> |
17 <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/> | 20 <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/> |
18 <param name="all_controls" label="Path to all unfiltered insertions from control sample" argument="--all_controls_path" type="data" format="gff3"/> | 21 <param name="all_controls" label="Path to all unfiltered insertions from control sample" argument="--all_controls_path" type="data" format="gff3"/> |
19 <param name="output_discard" label="Output discarded records? Thye will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/> | 22 <param name="output_discard" label="Output discarded records? Discarded records will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/> |
20 </inputs> | 23 </inputs> |
21 <outputs> | 24 <outputs> |
22 <data name="output" format="gff3"/> | 25 <data name="output" format="gff3"/> |
23 </outputs> | 26 </outputs> |
24 <tests> | 27 <tests> |