Mercurial > repos > mvdbeek > bam_readtagger
comparison filter_insertions.xml @ 64:190d64e5e32b draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit be63fdf98ea1aaa5009136c6b0f8c1311e53bb8e"
author | mvdbeek |
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date | Sun, 01 Sep 2019 16:30:54 -0400 |
parents | e675e6d349bd |
children | da97e0316abc |
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63:e675e6d349bd | 64:190d64e5e32b |
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1 <tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.10"> | 1 <tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.11"> |
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="0.5.10">readtagger</requirement> | 4 <requirement type="package" version="0.5.11">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 $all_insertions all_insertions.gff && |
16 #for i, p in enumerate($all_controls) | 16 #for i, p in enumerate($all_controls) |
17 --all_controls_paths all_controls_${i}.gff | 17 --all_controls_paths all_controls_${i}.gff |
18 #end for | 18 #end for |
19 --output_path '$output' | 19 --output_path '$output' |
20 $output_discard | 20 $output_discard |
21 --min_length $min_length | |
21 ]]></command> | 22 ]]></command> |
22 <inputs> | 23 <inputs> |
23 <param name="putative_insertions" label="Select dataset with filtered putative insertions" argument="--putative_insertions_path" type="data" format="gff3"/> | 24 <param name="putative_insertions" label="Select dataset with filtered putative insertions" argument="--putative_insertions_path" type="data" format="gff3"/> |
24 <param name="all_insertions" label="Select datasets with all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/> | 25 <param name="all_insertions" label="Select datasets with all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/> |
25 <param name="all_controls" label="Select datasets with all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/> | 26 <param name="all_controls" label="Select datasets with all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/> |
26 <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"/> | 27 <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"/> |
28 <param argument="--min_length" label="Minimum length necessary to match clip patterns" help="If too low will create false matches, if too high will not find legitimate matches." value="4" min="1" type="integer"/> | |
27 </inputs> | 29 </inputs> |
28 <outputs> | 30 <outputs> |
29 <data name="output" format="gff3"/> | 31 <data name="output" format="gff3"/> |
30 </outputs> | 32 </outputs> |
31 <tests> | 33 <tests> |