| Previous changeset 6:147465efa99c (2021-06-10) Next changeset 8:aea7008fe1f1 (2021-08-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a" |
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modified:
ivar_variants.xml |
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added:
test-data/zika/Z52_a_pass.vcf |
| b |
| diff -r 147465efa99c -r 252dfb042563 ivar_variants.xml --- a/ivar_variants.xml Thu Jun 10 22:06:04 2021 +0000 +++ b/ivar_variants.xml Fri Jun 11 15:42:14 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="ivar_variants" name="ivar variants" version="@VERSION@+galaxy1"> +<tool id="ivar_variants" name="ivar variants" version="@VERSION@+galaxy2"> <description>Call variants from aligned BAM file</description> <macros> <import>macros.xml</import> @@ -13,13 +13,14 @@ samtools mpileup -A -d 0 --reference ref.fa -B -Q 0 sorted.bam | ivar variants -p variants -q $min_qual - -t $min_freq && - #if str($output_format.choice) == 'vcf' - python '${__tool_directory__}/ivar_variants_to_vcf.py' + -t $min_freq + #if str($output_format.choice) == "tabular" or str($output_format.choice) == "tabular_and_vcf" + && cp variants.tsv '$output_variants_tabular' + #end if + #if str($output_format.choice) == 'vcf' or str($output_format.choice) == "tabular_and_vcf" + && python '${__tool_directory__}/ivar_variants_to_vcf.py' ${output_format.pass_only} - variants.tsv '$output_variants' - #else - cp variants.tsv '$output_variants' + variants.tsv '$output_variants_vcf' #end if ]]> </command> <inputs> @@ -31,25 +32,33 @@ <param name="choice" type="select" label="Output format"> <option value="tabular">Tabular (native tool output)</option> <option value="vcf">VCF</option> + <option value="tabular_and_vcf">Both Tabular and VCF</option> </param> <when value="vcf"> <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters" /> </when> + <when value="tabular_and_vcf"> + <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters" /> + </when> <when value="tabular" /> </conditional> </inputs> <outputs> - <data name="output_variants" format="tabular" label="${tool.name} on ${on_string}"> - <change_format> - <when input="output_format.choice" value="vcf" format="vcf" /> - </change_format> + <data name="output_variants_tabular" format="tabular" label="${tool.name} tabular output on ${on_string}"> + <filter>output_format['choice'] == 'tabular' or output_format['choice'] == 'tabular_and_vcf'</filter> + <actions> + <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA" /> + </actions> + </data> + <data name="output_variants_vcf" format="vcf" label="${tool.name} VCF on ${on_string}"> + <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter> </data> </outputs> <tests> <test expect_num_outputs="1"> <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" /> <param name="ref" value="zika/db/PRV.fa" /> - <output name="output_variants" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="10"/> + <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="10"/> </test> <test expect_num_outputs="1"> <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" /> @@ -57,8 +66,19 @@ <conditional name="output_format"> <param name="choice" value="vcf" /> </conditional> - <output name="output_variants" file="zika/Z52_a.vcf" ftype="vcf"/> + <output name="output_variants_vcf" file="zika/Z52_a.vcf" ftype="vcf"/> </test> + <test expect_num_outputs="2"> + <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" /> + <param name="ref" value="zika/db/PRV.fa" /> + <conditional name="output_format"> + <param name="choice" value="tabular_and_vcf" /> + <param name="pass_only" value="true" /> + </conditional> + <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="10"/> + <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/> + </test> + </tests> <help><![CDATA[ iVar uses the output of the samtools mpileup command to call variants - |
| b |
| diff -r 147465efa99c -r 252dfb042563 test-data/zika/Z52_a_pass.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/Z52_a_pass.vcf Fri Jun 11 15:42:14 2021 +0000 |
| b |
| @@ -0,0 +1,24 @@ +##fileformat=VCFv4.2 +##source=iVar +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> +##INFO=<ID=REF_DP,Number=1,Type=Integer,Description="Depth of reference base"> +##INFO=<ID=REF_RV,Number=1,Type=Integer,Description="Depth of reference base on reverse reads"> +##INFO=<ID=REF_QUAL,Number=1,Type=Integer,Description="Mean quality of reference base"> +##INFO=<ID=ALT_DP,Number=1,Type=Integer,Description="Depth of alternate base"> +##INFO=<ID=ALT_RV,Number=1,Type=Integer,Description="Deapth of alternate base on reverse reads"> +##INFO=<ID=ALT_QUAL,Number=1,Type=Integer,Description="Mean quality of alternate base"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Frequency of alternate base"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##FILTER=<ID=PASS,Description="Result of p-value <= 0.05"> +##FILTER=<ID=FAIL,Description="Result of p-value > 0.05"> +#CHROM POS ID REF ALT QUAL FILTER INFO +PRV 1682 . C T . PASS DP=1133;REF_DP=1097;REF_RV=984;REF_QUAL=37;ALT_DP=34;ALT_RV=33;ALT_QUAL=37;AF=0.0300088 +PRV 1965 . T G . PASS DP=365;REF_DP=302;REF_RV=113;REF_QUAL=37;ALT_DP=63;ALT_RV=25;ALT_QUAL=37;AF=0.172603 +PRV 2781 . T G . PASS DP=408;REF_DP=354;REF_RV=70;REF_QUAL=37;ALT_DP=48;ALT_RV=8;ALT_QUAL=36;AF=0.117647 +PRV 2922 . C T . PASS DP=275;REF_DP=264;REF_RV=0;REF_QUAL=36;ALT_DP=11;ALT_RV=0;ALT_QUAL=36;AF=0.04 +PRV 3148 . Y T . PASS DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=1324;ALT_RV=264;ALT_QUAL=36;AF=0.77563 +PRV 3148 . Y C . PASS DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=381;ALT_RV=75;ALT_QUAL=36;AF=0.223199 +PRV 3295 . A G . PASS DP=1040;REF_DP=1002;REF_RV=1002;REF_QUAL=35;ALT_DP=38;ALT_RV=38;ALT_QUAL=33;AF=0.0365385 +PRV 5680 . C T . PASS DP=35;REF_DP=27;REF_RV=5;REF_QUAL=44;ALT_DP=8;ALT_RV=2;ALT_QUAL=46;AF=0.228571 +PRV 7916 . C T . PASS DP=432;REF_DP=351;REF_RV=289;REF_QUAL=36;ALT_DP=81;ALT_RV=78;ALT_QUAL=37;AF=0.1875 +PRV 9713 . C T . PASS DP=387;REF_DP=374;REF_RV=0;REF_QUAL=37;ALT_DP=13;ALT_RV=0;ALT_QUAL=35;AF=0.0335917 |