Mercurial > repos > iuc > varscan_somatic
comparison varscan_somatic.xml @ 1:31a38ce7e8ae 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 09:19:25 -0400 |
parents | 72b8ce355fae |
children | 2fe9ebb98aad |
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0:72b8ce355fae | 1:31a38ce7e8ae |
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1 <tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.0"> | 1 <tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.1"> |
2 <description>Call germline/somatic variants from tumor-normal pileups</description> | 2 <description>Call germline/somatic variants 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 varscan somatic | 9 varscan somatic |
10 '${normal_pileup}' | 10 @INPUT_PILEUPS@ |
11 '${tumor_pileup}' | |
12 galaxy_out | |
13 --min-coverage ${min_coverage} | 11 --min-coverage ${min_coverage} |
14 --min-reads2 ${min_reads2} | 12 --min-reads2 ${min_reads2} |
15 --min-avg-qual ${min_avg_qual} | 13 --min-avg-qual ${min_avg_qual} |
16 --min-var-freq ${min_var_freq} | 14 --min-var-freq ${min_var_freq} |
17 --min-freq-for-hom ${min_freq_for_hom} | 15 --min-freq-for-hom ${min_freq_for_hom} |
27 | 25 |
28 --output-vcf 1 | 26 --output-vcf 1 |
29 ]]></command> | 27 ]]></command> |
30 | 28 |
31 <inputs> | 29 <inputs> |
32 <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/> | 30 |
33 <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/> | 31 <expand macro="input_pileups"/> |
34 | 32 |
35 <expand macro="min_coverage" /> | 33 <expand macro="min_coverage" /> |
36 <param argument="--min-coverage-normal" name="min_coverage_normal" type="integer" value="8" min="1" max="200" | 34 <param argument="--min-coverage-normal" name="min_coverage_normal" type="integer" value="8" min="1" max="200" |
37 label="Minimum read depth from the normal sample" help="Minimum depth at a position to make a call" /> | 35 label="Minimum read depth from the normal sample" help="Minimum depth at a position to make a call" /> |
38 <param argument="--min-coverage-tumor" name="min_coverage_tumor" type="integer" value="6" min="1" max="200" | 36 <param argument="--min-coverage-tumor" name="min_coverage_tumor" type="integer" value="6" min="1" max="200" |
54 <data name="output_indel" from_work_dir="galaxy_out.indel.vcf" format="vcf"/> | 52 <data name="output_indel" from_work_dir="galaxy_out.indel.vcf" format="vcf"/> |
55 <data name="output_snp" from_work_dir="galaxy_out.snp.vcf" format="vcf"/> | 53 <data name="output_snp" from_work_dir="galaxy_out.snp.vcf" format="vcf"/> |
56 </outputs> | 54 </outputs> |
57 <tests> | 55 <tests> |
58 <test> | 56 <test> |
59 <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" /> | 57 <conditional name="pileup"> |
60 <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" /> | 58 <param name="pileup_select" value="separated" /> |
59 <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" /> | |
60 <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" /> | |
61 </conditional> | |
61 <param name="min_coverage" value="2" /> | 62 <param name="min_coverage" value="2" /> |
62 <param name="min_coverage_normal" value="2" /> | 63 <param name="min_coverage_normal" value="2" /> |
63 <param name="min_coverage_tumor" value="2" /> | 64 <param name="min_coverage_tumor" value="2" /> |
64 <param name="min_reads2" value="1" /> | 65 <param name="min_reads2" value="1" /> |
65 <param name="min_avg_qual" value="5" /> | 66 <param name="min_avg_qual" value="5" /> |
68 <param name="normal_purity" value="0.6" /> | 69 <param name="normal_purity" value="0.6" /> |
69 <param name="tumor_purity" value="0.6" /> | 70 <param name="tumor_purity" value="0.6" /> |
70 <param name="p_value" value="0.99" /> | 71 <param name="p_value" value="0.99" /> |
71 <output name="output_indel" file="varscan_somatic_indel_result1.vcf" lines_diff="0" /> | 72 <output name="output_indel" file="varscan_somatic_indel_result1.vcf" lines_diff="0" /> |
72 <output name="output_snp" file="varscan_somatic_snp_result1.vcf" lines_diff="0" /> | 73 <output name="output_snp" file="varscan_somatic_snp_result1.vcf" lines_diff="0" /> |
74 </test> | |
75 <test> | |
76 <conditional name="pileup"> | |
77 <param name="pileup_select" value="combined" /> | |
78 <param name="combined_pileup" value="NT.pileup.gz" /> | |
79 </conditional> | |
80 <param name="min_coverage" value="2" /> | |
81 <param name="min_coverage_normal" value="2" /> | |
82 <param name="min_coverage_tumor" value="2" /> | |
83 <param name="min_reads2" value="1" /> | |
84 <param name="min_avg_qual" value="5" /> | |
85 <param name="min_var_freq" value="0.01" /> | |
86 <param name="min_freq_for_hom" value="0.75" /> | |
87 <param name="normal_purity" value="0.6" /> | |
88 <param name="tumor_purity" value="0.6" /> | |
89 <param name="p_value" value="0.99" /> | |
90 <output name="output_indel" file="varscan_somatic_indel_result2.vcf" lines_diff="0" /> | |
91 <output name="output_snp" file="varscan_somatic_snp_result2.vcf" lines_diff="0" /> | |
73 </test> | 92 </test> |
74 </tests> | 93 </tests> |
75 | 94 |
76 <help> | 95 <help> |
77 **VarScan Overview** | 96 **VarScan Overview** |