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changeset 0:fc75be7f3fd2 draft

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planemo upload for repository https://github.com/COMBAT-TB/vcf_snps_utils commit a7c330a5dff63e78b9ff963a0b380937d27f4449
author sanbi-uwc
date Thu, 16 Aug 2018 07:41:03 -0400
parents
children f8f16a682d01
files intersect.xml test-data/1.bed test-data/1_bed_random_lines_1_seed_asdf_out.bed vcf_snps_utils_macros.xml
diffstat 4 files changed, 144 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/intersect.xml	Thu Aug 16 07:41:03 2018 -0400
@@ -0,0 +1,69 @@
+ <?xml version="1.0"?>
+<tool id="intersect" name="Intersect SNPs with a CSV file" version="@TOOL_VERSION@+galaxy0" profile="17.01">
+  <description>Intersect SNPs with a CSV file</description>
+   <macros>
+    <import>vcf_snps_utils_macros.xml</import>
+  </macros>
+        
+  <command detect_errors="exit_code"><![CDATA[
+    ln -s '$input_vcf' data.vcf &&
+    ln -s '$input_csv' data.csv &&
+    vcf_snps_utils intersect data.vcf data.csv --out "$output_pdf.file.path"
+    ]]>
+  </command>
+        
+  <inputs>
+    <param name="input_vcf" type="data" format="vcf" label="Input VCF" />
+    <param name="input_csv" type="data" format="csv" label="Input CSV" />
+  </inputs>
+        
+  <outputs>
+    <data name="output_pdf" format="pdf" label="SNPs Intersection Report" />
+    <data name="output_txt" format="txt" label="SNPs Intersection Combination Report" />
+    <data name="output_r" format="R" label="SNPs Intersection R object" />
+  </outputs>
+        
+  <tests>
+    <test>
+      <param name="input_vcf" value="sample1.vcf" />
+      <output name="output" compare="diff" lines_diff="2" file="sample1.html" ftype="html" />
+    </test>
+
+  <help>
+
+**What it does**
+
+Intersect SNPs and generate an output report from a CSV file of knowned SNPs (workflow generated/annotated)
+
+Usage: vcf_snps_utils intersect [OPTIONS] [VCFFILES]... CSVFILE
+
+-----
+
+**Example**
+
+  VCF snp intersect tool (CSV file).
+
+  This tools compares CSV snps to the VCF snps This is to establish whether
+  the discovered (VCF snps) have been discovered in the pass. This will
+  potential be extended to include verification using other external source
+  such as databases/api.
+
+  CSV File passed should be in the following format (Example):
+  position in H37Rv        gene    short name      snp_type        Reference       Sample1   Sample2       Sample3
+  1285     dnaA    dnaA1285        nsSNP   G       G       G       G
+  4013     recF    recF4013        nsSNP   T       C       C       C
+
+  Report bugs to: combattb-help@sanbi.ac.za CombatTB home page:
+  <http://www.combattb.org/software/tools/> General help using CombatTB
+  software: <http://www.combattb.org/gethelp/>
+
+Options:
+  --out TEXT  set the output directory, default is
+              "/tmp/vcf_snps_utils_output/"
+  --help      Show this message and exit.
+
+  vcf_snps_utils intersect example.vcf example.csv --out output/test
+
+    </help>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.bed	Thu Aug 16 07:41:03 2018 -0400
@@ -0,0 +1,65 @@
+chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-
+chr1	147984545	147984630	CCDS990.1_cds_0_0_chr1_147984546_f	0	+
+chr1	148078400	148078582	CCDS993.1_cds_0_0_chr1_148078401_r	0	-
+chr1	148185136	148185276	CCDS996.1_cds_0_0_chr1_148185137_f	0	+
+chr10	55251623	55253124	CCDS7248.1_cds_0_0_chr10_55251624_r	0	-
+chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-
+chr11	116206508	116206563	CCDS8377.1_cds_0_0_chr11_116206509_f	0	+
+chr11	116211733	116212337	CCDS8378.1_cds_0_0_chr11_116211734_r	0	-
+chr11	1812377	1812407	CCDS7726.1_cds_0_0_chr11_1812378_f	0	+
+chr12	38440094	38440321	CCDS8736.1_cds_0_0_chr12_38440095_r	0	-
+chr13	112381694	112381953	CCDS9526.1_cds_0_0_chr13_112381695_f	0	+
+chr14	98710240	98712285	CCDS9949.1_cds_0_0_chr14_98710241_r	0	-
+chr15	41486872	41487060	CCDS10096.1_cds_0_0_chr15_41486873_r	0	-
+chr15	41673708	41673857	CCDS10097.1_cds_0_0_chr15_41673709_f	0	+
+chr15	41679161	41679250	CCDS10098.1_cds_0_0_chr15_41679162_r	0	-
+chr15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+
+chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+
+chr16	179963	180135	CCDS10401.1_cds_0_0_chr16_179964_r	0	-
+chr16	244413	244681	CCDS10402.1_cds_0_0_chr16_244414_f	0	+
+chr16	259268	259383	CCDS10403.1_cds_0_0_chr16_259269_r	0	-
+chr18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-
+chr18	59406881	59407046	CCDS11985.1_cds_0_0_chr18_59406882_f	0	+
+chr18	59455932	59456337	CCDS11986.1_cds_0_0_chr18_59455933_r	0	-
+chr18	59600586	59600754	CCDS11988.1_cds_0_0_chr18_59600587_f	0	+
+chr19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+
+chr19	59236026	59236146	CCDS12872.1_cds_0_0_chr19_59236027_r	0	-
+chr19	59297998	59298008	CCDS12877.1_cds_0_0_chr19_59297999_f	0	+
+chr19	59302168	59302288	CCDS12878.1_cds_0_0_chr19_59302169_r	0	-
+chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+
+chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_r	0	-
+chr2	220190202	220190242	CCDS2441.1_cds_0_0_chr2_220190203_f	0	+
+chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-
+chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-
+chr20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+
+chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-
+chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+
+chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+
+chr21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-
+chr21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+
+chr21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-
+chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+
+chr22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-
+chr22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+
+chr22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_r	0	-
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+
+chr5	131556601	131556672	CCDS4151.1_cds_0_0_chr5_131556602_r	0	-
+chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+
+chr5	131847541	131847666	CCDS4155.1_cds_0_0_chr5_131847542_r	0	-
+chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-
+chr6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+
+chr6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-
+chr6	108722976	108723115	CCDS5067.1_cds_0_0_chr6_108722977_f	0	+
+chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+
+chr7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-
+chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+
+chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	0	-
+chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-
+chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+
+chr9	128787519	128789136	CCDS6915.1_cds_0_0_chr9_128787520_r	0	-
+chr9	128882427	128882523	CCDS6917.1_cds_0_0_chr9_128882428_f	0	+
+chr9	128937229	128937445	CCDS6919.1_cds_0_0_chr9_128937230_r	0	-
+chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_f	0	+
+chrX	152648964	152649196	CCDS14733.1_cds_0_0_chrX_152648965_r	0	-
+chrX	152691446	152691471	CCDS14735.1_cds_0_0_chrX_152691447_f	0	+
+chrX	152694029	152694263	CCDS14736.1_cds_0_0_chrX_152694030_r	0	-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1_bed_random_lines_1_seed_asdf_out.bed	Thu Aug 16 07:41:03 2018 -0400
@@ -0,0 +1,1 @@
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcf_snps_utils_macros.xml	Thu Aug 16 07:41:03 2018 -0400
@@ -0,0 +1,9 @@
+<macros>
+  <token name="@TOOL_VERSION@">0.0.2</token>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="@TOOL_VERSION@">vcf_snps_utils</requirement>
+      <yield />
+    </requirements>    
+  </xml>
+</macros>
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