Mercurial > repos > mvdbeek > bam_readtagger
comparison filter_insertions.xml @ 41:4fdf606153df draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 89e57ebe9ad1eb4ba44167f83935869fb54b8396-dirty
| author | mvdbeek |
|---|---|
| date | Thu, 24 May 2018 11:05:38 -0400 |
| parents | 4b1ebfcd0f46 |
| children | 5b8781514bc1 |
comparison
equal
deleted
inserted
replaced
| 40:4b1ebfcd0f46 | 41:4fdf606153df |
|---|---|
| 1 <tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.10"> | 1 <tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.11"> |
| 2 <description>based on softclips in control files</description> | 2 <description>based on softclips in control files</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.4.10">readtagger</requirement> | 4 <requirement type="package" version="0.4.11">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 && | 8 ln -fs $putative_insertions putative_insertions.gff && |
| 9 ln -fs $all_insertions all_insertions.gff && | 9 ln -fs $all_insertions all_insertions.gff && |
| 10 ln -fs $all_controls all_controls_path.gff && | 10 ln -fs $all_controls all_controls_path.gff && |
| 11 confirm_insertions | 11 confirm_insertions |
| 12 --putative_insertions_path putative_insertions.gff | 12 --putative_insertions_path putative_insertions.gff |
| 13 --all_treatments_path all_insertions.gff | 13 --all_treatments_path all_insertions.gff |
| 14 --all_controls_path all_controls_path.gff | 14 #for p in $all_controls |
| 15 --all_controls_paths '$p' | |
| 16 #end for | |
| 15 --output_path '$output' | 17 --output_path '$output' |
| 16 $output_discard | 18 $output_discard |
| 17 ]]></command> | 19 ]]></command> |
| 18 <inputs> | 20 <inputs> |
| 19 <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/> | 21 <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/> |
| 20 <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/> | 22 <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_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"/> | 23 <param name="all_controls" label="Path to all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/> |
| 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"/> | 24 <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"/> |
| 23 </inputs> | 25 </inputs> |
| 24 <outputs> | 26 <outputs> |
| 25 <data name="output" format="gff3"/> | 27 <data name="output" format="gff3"/> |
| 26 </outputs> | 28 </outputs> |