Mercurial > repos > iuc > varscan_somatic

changeset 1:31a38ce7e8ae draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
author iuc
date Sun, 15 Jul 2018 09:19:25 -0400
parents 72b8ce355fae
children 2fe9ebb98aad
files macros.xml 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 varscan_somatic.xml
diffstat 6 files changed, 109 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Jul 10 13:35:40 2018 -0400
+++ b/macros.xml	Sun Jul 15 09:19:25 2018 -0400
@@ -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"/>
Binary file test-data/NT.pileup.gz has changed
--- /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
@@ -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
--- /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
@@ -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
--- /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
@@ -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
--- a/varscan_somatic.xml	Tue Jul 10 13:35:40 2018 -0400
+++ b/varscan_somatic.xml	Sun Jul 15 09:19:25 2018 -0400
@@ -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>