Mercurial > repos > iuc > snippy
changeset 3:feb7e635c6af draft
planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
| author | iuc |
|---|---|
| date | Tue, 02 Apr 2019 17:21:50 -0400 |
| parents | 776ebd1239da |
| children | 9bccc8404a3c |
| files | snippy.xml test-data/b_2_fna_ref_mincov_2_minqual_60.snps.gff |
| diffstat | 2 files changed, 24 insertions(+), 13 deletions(-) [+] |
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--- a/snippy.xml Mon Mar 18 10:59:29 2019 -0400 +++ b/snippy.xml Tue Apr 02 17:21:50 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="snippy" name="snippy" version="@VERSION@+galaxy1"> +<tool id="snippy" name="snippy" version="@VERSION@+galaxy2"> <description> Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. </description> @@ -40,16 +40,13 @@ #if str( $fastq_input.fastq_input_selector ) == "paired" --R1 '$fastq_input.fastq_input1' --R2 '$fastq_input.fastq_input2' - #end if - #if str( $fastq_input.fastq_input_selector ) == "paired_collection" + #elif str( $fastq_input.fastq_input_selector ) == "paired_collection" --R1 '$fastq_input.fastq_input.forward' --R2 '$fastq_input.fastq_input.reverse' - #end if - #if str( $fastq_input.fastq_input_selector ) == "single" - --se '$fastq_input.fastq_input' - #end if - #if str( $fastq_input.fastq_input_selector ) == "paired_iv" - --peil '$fastq_input.fastq_input' + #elif str( $fastq_input.fastq_input_selector ) == "single" + --se '$fastq_input.fastq_input_single' + #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" + --peil '$fastq_input.fastq_input_interleaved' #end if && @@ -59,8 +56,10 @@ #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier) #elif str( $fastq_input.fastq_input_selector ) == "paired_collection" #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name) - #else - #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier) + #elif str( $fastq_input.fastq_input_selector ) == "single" + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier) + #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier) #end if mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ && @@ -88,13 +87,13 @@ <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/> </when> <when value="single"> - <param name="fastq_input" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/> + <param name="fastq_input_single" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/> </when> <when value="paired_collection"> <param name="fastq_input" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> </when> <when value="paired_iv"> - <param name="fastq_input" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> + <param name="fastq_input_interleaved" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> </when> </conditional> @@ -200,6 +199,16 @@ <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" /> </test> + <test> <!-- test 3 - fasta ref one snp single --> + <param name="ref" value="reference.fasta" ftype="fasta" /> + <param name="fastq_input_selector" value="single" /> + <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" /> + <param name="mincov" value="2" /> + <param name="minqual" value="60" /> + <param name="outputs" value="outgff,outsum" /> + <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" /> + <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" /> + </test> </tests>