| Previous changeset 0:72b8ce355fae (2018-07-10) Next changeset 2:2fe9ebb98aad (2018-12-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177 |
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modified:
macros.xml varscan_somatic.xml |
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added:
test-data/NT.pileup.gz test-data/varscan_copynumber_result2.interval test-data/varscan_somatic_indel_result2.vcf test-data/varscan_somatic_snp_result2.vcf |
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| diff -r 72b8ce355fae -r 31a38ce7e8ae macros.xml --- a/macros.xml Tue Jul 10 13:35:40 2018 -0400 +++ b/macros.xml Sun Jul 15 09:19:25 2018 -0400 |
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| @@ -23,6 +23,35 @@ </citations> </xml> + <xml name="input_pileups"> + <conditional name="pileup"> + <param name="pileup_select" type="select" label="How do you want to provide your pileup files?" help=""> + <option value="separated">As separated normal and tumor files</option> + <option value="combined">Normal and Tumor combined in one file</option> + </param> + <when value="separated"> + <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset for Normal" help=""/> + <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset for Tumor" help=""/> + </when> + <when value="combined"> + <param name="combined_pileup" format="pileup" type="data" label="Samtools pileup dataset which has combined Normal and Tumor samples" help=""/> + </when> + </conditional> + </xml> + + <token name="@INPUT_PILEUPS@"> + #if $pileup.pileup_select == 'separated' + '${pileup.normal_pileup}' + '${pileup.tumor_pileup}' + galaxy_out + #else: + '${pileup.combined_pileup}' + galaxy_out + --mpileup 1 + #end if + + </token> + <xml name="min_coverage"> <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200" label="Minimum read depth" help="Minimum depth at a position to make a call"/> |
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| diff -r 72b8ce355fae -r 31a38ce7e8ae test-data/NT.pileup.gz |
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| Binary file test-data/NT.pileup.gz has changed |
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| diff -r 72b8ce355fae -r 31a38ce7e8ae test-data/varscan_copynumber_result2.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/varscan_copynumber_result2.interval Sun Jul 15 09:19:25 2018 -0400 |
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| @@ -0,0 +1,9 @@ +chrom chr_start chr_stop num_positions normal_depth tumor_depth log2_ratio gc_content +chr1 51436045 51436144 100 26.9 25.9 -0.052 51.0 +chr1 51436145 51436214 70 27.6 30.3 0.134 45.7 +chr1 51439427 51439526 100 31.1 29.3 -0.086 36.0 +chr1 51439527 51439626 100 85.3 86.0 0.012 44.0 +chr1 51439627 51439726 100 107.2 108.0 0.011 46.0 +chr1 51439727 51439826 100 70.8 80.3 0.183 58.0 +chr1 51439827 51439926 100 46.3 53.3 0.202 60.0 +chr1 51439927 51439960 34 27.5 35.9 0.383 52.9 |
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| diff -r 72b8ce355fae -r 31a38ce7e8ae test-data/varscan_somatic_indel_result2.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/varscan_somatic_indel_result2.vcf Sun Jul 15 09:19:25 2018 -0400 |
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| @@ -0,0 +1,18 @@ +##fileformat=VCFv4.1 +##source=VarScan2 +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases"> +##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation"> +##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)"> +##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value"> +##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls"> +##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls"> +##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> +##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> +##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> +##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR |
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| diff -r 72b8ce355fae -r 31a38ce7e8ae test-data/varscan_somatic_snp_result2.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/varscan_somatic_snp_result2.vcf Sun Jul 15 09:19:25 2018 -0400 |
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| @@ -0,0 +1,26 @@ +##fileformat=VCFv4.1 +##source=VarScan2 +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases"> +##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation"> +##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)"> +##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value"> +##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls"> +##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls"> +##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> +##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)"> +##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> +##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR +chr1 51436072 . C A . PASS DP=47;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.4681E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:26:26:0:0%:23,3,0,0 0/1:.:21:20:1:4.76%:19,1,1,0 +chr1 51436311 . T C . PASS DP=16;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.375E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:9:9:0:0%:1,8,0,0 0/1:.:7:6:1:14.29%:0,6,0,1 +chr1 51436320 . G A . PASS DP=19;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.2632E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:9:9:0:0%:1,8,0,0 0/1:.:10:9:1:10%:0,9,0,1 +chr1 51439665 . C T . PASS DP=226;SOMATIC;SS=2;SSC=9;GPV=1E0;SPV=1.2006E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:114:114:0:0%:56,58,0,0 0/1:.:112:109:3:2.68%:63,46,2,1 +chr1 51439763 . G A . PASS DP=159;SOMATIC;SS=2;SSC=5;GPV=1E0;SPV=2.7092E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:76:76:0:0%:34,42,0,0 0/1:.:83:81:2:2.41%:32,49,1,1 +chr1 51440025 . A C . PASS DP=27;SOMATIC;SS=2;SSC=1;GPV=1E0;SPV=6.6667E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:9:9:0:0%:1,8,0,0 0/1:.:18:17:1:5.56%:1,16,0,1 +chr1 51440035 . G T . PASS DP=21;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=6.1905E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:8:8:0:0%:1,7,0,0 0/1:.:13:12:1:7.69%:1,11,0,1 +chr1 51440056 . T G . PASS DP=22;SOMATIC;SS=2;SSC=1;GPV=1E0;SPV=6.3636E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:8:8:0:0%:1,7,0,0 0/1:.:14:13:1:7.14%:1,12,0,1 |
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| diff -r 72b8ce355fae -r 31a38ce7e8ae varscan_somatic.xml --- a/varscan_somatic.xml Tue Jul 10 13:35:40 2018 -0400 +++ b/varscan_somatic.xml Sun Jul 15 09:19:25 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.0"> +<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.1"> <description>Call germline/somatic variants from tumor-normal pileups</description> <macros> <import>macros.xml</import> @@ -7,9 +7,7 @@ <expand macro="stdio" /> <command><![CDATA[ varscan somatic - '${normal_pileup}' - '${tumor_pileup}' - galaxy_out + @INPUT_PILEUPS@ --min-coverage ${min_coverage} --min-reads2 ${min_reads2} --min-avg-qual ${min_avg_qual} @@ -29,8 +27,8 @@ ]]></command> <inputs> - <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/> - <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/> + + <expand macro="input_pileups"/> <expand macro="min_coverage" /> <param argument="--min-coverage-normal" name="min_coverage_normal" type="integer" value="8" min="1" max="200" @@ -56,8 +54,11 @@ </outputs> <tests> <test> - <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" /> - <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" /> + <conditional name="pileup"> + <param name="pileup_select" value="separated" /> + <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" /> + <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" /> + </conditional> <param name="min_coverage" value="2" /> <param name="min_coverage_normal" value="2" /> <param name="min_coverage_tumor" value="2" /> @@ -71,6 +72,24 @@ <output name="output_indel" file="varscan_somatic_indel_result1.vcf" lines_diff="0" /> <output name="output_snp" file="varscan_somatic_snp_result1.vcf" lines_diff="0" /> </test> + <test> + <conditional name="pileup"> + <param name="pileup_select" value="combined" /> + <param name="combined_pileup" value="NT.pileup.gz" /> + </conditional> + <param name="min_coverage" value="2" /> + <param name="min_coverage_normal" value="2" /> + <param name="min_coverage_tumor" value="2" /> + <param name="min_reads2" value="1" /> + <param name="min_avg_qual" value="5" /> + <param name="min_var_freq" value="0.01" /> + <param name="min_freq_for_hom" value="0.75" /> + <param name="normal_purity" value="0.6" /> + <param name="tumor_purity" value="0.6" /> + <param name="p_value" value="0.99" /> + <output name="output_indel" file="varscan_somatic_indel_result2.vcf" lines_diff="0" /> + <output name="output_snp" file="varscan_somatic_snp_result2.vcf" lines_diff="0" /> + </test> </tests> <help> |