Mercurial > repos > iuc > snippy
comparison snippy.xml @ 3:feb7e635c6af draft
planemo upload commit f7ba9aa90e952d0639fba2cf6674bb4a7523f308
| author | iuc |
|---|---|
| date | Tue, 02 Apr 2019 17:21:50 -0400 |
| parents | 776ebd1239da |
| children | 0aa87d97847f |
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| 2:776ebd1239da | 3:feb7e635c6af |
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| 1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy1"> | 1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy2"> |
| 2 <description> | 2 <description> |
| 3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. | 3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. |
| 4 </description> | 4 </description> |
| 5 <macros> | 5 <macros> |
| 6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
| 38 #end if | 38 #end if |
| 39 | 39 |
| 40 #if str( $fastq_input.fastq_input_selector ) == "paired" | 40 #if str( $fastq_input.fastq_input_selector ) == "paired" |
| 41 --R1 '$fastq_input.fastq_input1' | 41 --R1 '$fastq_input.fastq_input1' |
| 42 --R2 '$fastq_input.fastq_input2' | 42 --R2 '$fastq_input.fastq_input2' |
| 43 #end if | 43 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection" |
| 44 #if str( $fastq_input.fastq_input_selector ) == "paired_collection" | |
| 45 --R1 '$fastq_input.fastq_input.forward' | 44 --R1 '$fastq_input.fastq_input.forward' |
| 46 --R2 '$fastq_input.fastq_input.reverse' | 45 --R2 '$fastq_input.fastq_input.reverse' |
| 47 #end if | 46 #elif str( $fastq_input.fastq_input_selector ) == "single" |
| 48 #if str( $fastq_input.fastq_input_selector ) == "single" | 47 --se '$fastq_input.fastq_input_single' |
| 49 --se '$fastq_input.fastq_input' | 48 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" |
| 50 #end if | 49 --peil '$fastq_input.fastq_input_interleaved' |
| 51 #if str( $fastq_input.fastq_input_selector ) == "paired_iv" | |
| 52 --peil '$fastq_input.fastq_input' | |
| 53 #end if | 50 #end if |
| 54 | 51 |
| 55 && | 52 && |
| 56 | 53 |
| 57 #import re | 54 #import re |
| 58 #if str( $fastq_input.fastq_input_selector ) == "paired" | 55 #if str( $fastq_input.fastq_input_selector ) == "paired" |
| 59 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier) | 56 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier) |
| 60 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection" | 57 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection" |
| 61 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name) | 58 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name) |
| 62 #else | 59 #elif str( $fastq_input.fastq_input_selector ) == "single" |
| 63 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier) | 60 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier) |
| 61 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" | |
| 62 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier) | |
| 64 #end if | 63 #end if |
| 65 | 64 |
| 66 mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ && | 65 mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ && |
| 67 tar -czf out.tgz ${dir_name} | 66 tar -czf out.tgz ${dir_name} |
| 68 #if "outcon" in str($outputs) and $adv.rename_cons | 67 #if "outcon" in str($outputs) and $adv.rename_cons |
| 86 <when value="paired"> | 85 <when value="paired"> |
| 87 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/> | 86 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/> |
| 88 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/> | 87 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/> |
| 89 </when> | 88 </when> |
| 90 <when value="single"> | 89 <when value="single"> |
| 91 <param name="fastq_input" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/> | 90 <param name="fastq_input_single" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/> |
| 92 </when> | 91 </when> |
| 93 <when value="paired_collection"> | 92 <when value="paired_collection"> |
| 94 <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"/> | 93 <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"/> |
| 95 </when> | 94 </when> |
| 96 <when value="paired_iv"> | 95 <when value="paired_iv"> |
| 97 <param name="fastq_input" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> | 96 <param name="fastq_input_interleaved" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> |
| 98 </when> | 97 </when> |
| 99 </conditional> | 98 </conditional> |
| 100 | 99 |
| 101 <section name="adv" title="Advanced parameters" expanded="false"> | 100 <section name="adv" title="Advanced parameters" expanded="false"> |
| 102 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" /> | 101 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" /> |
| 198 <param name="outputs" value="outgff,outsum" /> | 197 <param name="outputs" value="outgff,outsum" /> |
| 199 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" /> | 198 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" /> |
| 200 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" /> | 199 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" /> |
| 201 </test> | 200 </test> |
| 202 | 201 |
| 202 <test> <!-- test 3 - fasta ref one snp single --> | |
| 203 <param name="ref" value="reference.fasta" ftype="fasta" /> | |
| 204 <param name="fastq_input_selector" value="single" /> | |
| 205 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" /> | |
| 206 <param name="mincov" value="2" /> | |
| 207 <param name="minqual" value="60" /> | |
| 208 <param name="outputs" value="outgff,outsum" /> | |
| 209 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" /> | |
| 210 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" /> | |
| 211 </test> | |
| 203 </tests> | 212 </tests> |
| 204 | 213 |
| 205 | 214 |
| 206 <help><![CDATA[ | 215 <help><![CDATA[ |
| 207 | 216 |