Mercurial > repos > iuc > varscan_copynumber
comparison varscan_copynumber.xml @ 1:8d8de66233ea draft
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
author | iuc |
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date | Sun, 15 Jul 2018 09:19:48 -0400 |
parents | a584f046e4a7 |
children | 4ce3441c407c |
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0:a584f046e4a7 | 1:8d8de66233ea |
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1 <tool id="varscan_copynumber" name="VarScan copynumber" version="@VERSION@.0"> | 1 <tool id="varscan_copynumber" name="VarScan copynumber" version="@VERSION@.1"> |
2 <description>Determine relative tumor copy number from tumor-normal pileups</description> | 2 <description>Determine relative tumor copy number from tumor-normal pileups</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <expand macro="stdio" /> | 7 <expand macro="stdio" /> |
8 <command><![CDATA[ | 8 <command><![CDATA[ |
9 | 9 |
10 varscan copynumber | 10 varscan copynumber |
11 '${normal_pileup}' | 11 @INPUT_PILEUPS@ |
12 '${tumor_pileup}' | |
13 galaxy_out | |
14 --min-coverage ${min_coverage} | 12 --min-coverage ${min_coverage} |
15 --min-base-qual ${min_base_qual} | 13 --min-base-qual ${min_base_qual} |
16 --min-map-qual ${min_map_qual} | 14 --min-map-qual ${min_map_qual} |
17 | 15 |
18 --min-segment-size ${min_segment_size} | 16 --min-segment-size ${min_segment_size} |
21 --data-ratio ${data_ratio} | 19 --data-ratio ${data_ratio} |
22 | 20 |
23 ]]></command> | 21 ]]></command> |
24 | 22 |
25 <inputs> | 23 <inputs> |
26 <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/> | 24 <expand macro="input_pileups"/> |
27 <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/> | |
28 | 25 |
29 <param argument="--min-coverage" name="min_coverage" type="integer" value="20" min="1" max="200" | 26 <param argument="--min-coverage" name="min_coverage" type="integer" value="20" min="1" max="200" |
30 label="Minimum read depth" help="Minimum coverage threshold for copynumber segments"/> | 27 label="Minimum read depth" help="Minimum coverage threshold for copynumber segments"/> |
31 | 28 |
32 <param argument="--min-base-qual" name="min_base_qual" type="integer" value="20" min="1" max="200" | 29 <param argument="--min-base-qual" name="min_base_qual" type="integer" value="20" min="1" max="200" |
50 <outputs> | 47 <outputs> |
51 <data name="output" from_work_dir="galaxy_out.copynumber" format="interval"/> | 48 <data name="output" from_work_dir="galaxy_out.copynumber" format="interval"/> |
52 </outputs> | 49 </outputs> |
53 <tests> | 50 <tests> |
54 <test> | 51 <test> |
55 <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" /> | 52 <conditional name="pileup"> |
56 <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" /> | 53 <param name="pileup_select" value="separated" /> |
54 <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" /> | |
55 <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" /> | |
56 </conditional> | |
57 <output name="output" file="varscan_copynumber_result1.interval" lines_diff="0" /> | 57 <output name="output" file="varscan_copynumber_result1.interval" lines_diff="0" /> |
58 </test> | |
59 <test> | |
60 <conditional name="pileup"> | |
61 <param name="pileup_select" value="combined" /> | |
62 <param name="combined_pileup" value="NT.pileup.gz" /> | |
63 </conditional> | |
64 <output name="output" file="varscan_copynumber_result2.interval" lines_diff="0" /> | |
58 </test> | 65 </test> |
59 </tests> | 66 </tests> |
60 | 67 |
61 <help> | 68 <help> |
62 **VarScan Overview** | 69 **VarScan Overview** |