Mercurial > repos > mvdbeek > bam_readtagger
comparison filter_insertions.xml @ 38:f6311a04a6c9 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
author | mvdbeek |
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date | Thu, 15 Mar 2018 05:13:22 -0400 |
parents | |
children | 432bb619c079 |
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37:93f7962a3e19 | 38:f6311a04a6c9 |
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1 <tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.9"> | |
2 <description>based on softclips in control files</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.4.9">readtagger</requirement> | |
5 </requirements> | |
6 <version_command>confirm_insertions --version</version_command> | |
7 <command detect_errors="aggressive"><![CDATA[ | |
8 confirm_insertions | |
9 --putative_insertions_path '$putative_insertions' | |
10 --all_treatments_path '$all_insertions' | |
11 --all_controls_path '$all_controls' | |
12 --output_path '$output' | |
13 $output_discard | |
14 ]]></command> | |
15 <inputs> | |
16 <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"/> | |
18 <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"/> | |
20 </inputs> | |
21 <outputs> | |
22 <data name="output" format="gff3"/> | |
23 </outputs> | |
24 <tests> | |
25 <test> | |
26 <param name="putative_insertions" value="putative_insertions.gff" ftype="gff3"/> | |
27 <param name="all_insertions" value="all_treatment_insertions.gff" ftype="gff3"/> | |
28 <param name="all_controls" value="all_control_insertions.gff" ftype="gff3"/> | |
29 <output name="output" file="confirmed_insertions.gff" ftype="gff3"/> | |
30 </test> | |
31 </tests> | |
32 <help><![CDATA[ | |
33 .. code-block:: | |
34 | |
35 | |
36 Usage: confirm_insertions [OPTIONS] | |
37 | |
38 Confirm insertions by checking that control file does not contain the same | |
39 clipping pattern. | |
40 | |
41 Options: | |
42 -p, --putative_insertions_path PATH | |
43 Path to file containing putative somatic | |
44 insertions [required] | |
45 -t, --all_treatments_path PATH Path to file containing all treatment | |
46 insertions [required] | |
47 -c, --all_controls_path PATH Path to file containing all control | |
48 insertions [required] | |
49 -o, --output_path TEXT Write annotated output to this Path. | |
50 --output_discarded_records / --no_output_discarded_records | |
51 Discard an alternative flag if the current | |
52 read is in a proper pair. | |
53 --version Show the version and exit. | |
54 --help Show this message and exit. | |
55 ]]></help> | |
56 </tool> |