Mercurial > repos > iuc > snippy
comparison snippy.xml @ 12:fa016f1eea1a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 7dec701af24e00b3328459f0a823eefd461237bb"
| author | iuc |
|---|---|
| date | Wed, 07 Apr 2021 11:24:48 +0000 |
| parents | 5bbf9eada9c2 |
| children |
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| 11:5bbf9eada9c2 | 12:fa016f1eea1a |
|---|---|
| 1 <tool id="snippy" name="snippy" version="@VERSION@"> | 1 <tool id="snippy" name="snippy" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@"> |
| 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> |
| 67 <option value="single">Single</option> | 67 <option value="single">Single</option> |
| 68 <option value="paired_collection">Paired Collection</option> | 68 <option value="paired_collection">Paired Collection</option> |
| 69 <option value="paired_iv">Paired Interleaved</option> | 69 <option value="paired_iv">Paired Interleaved</option> |
| 70 </param> | 70 </param> |
| 71 <when value="paired"> | 71 <when value="paired"> |
| 72 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/> | 72 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select first set of reads" help="Specify dataset with forward reads"/> |
| 73 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/> | 73 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/> |
| 74 </when> | 74 </when> |
| 75 <when value="single"> | 75 <when value="single"> |
| 76 <param name="fastq_input_single" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/> | 76 <param name="fastq_input_single" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select fastq dataset" help="Specify dataset with single reads"/> |
| 77 </when> | 77 </when> |
| 78 <when value="paired_collection"> | 78 <when value="paired_collection"> |
| 79 <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"/> | 79 <param name="fastq_input" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> |
| 80 </when> | 80 </when> |
| 81 <when value="paired_iv"> | 81 <when value="paired_iv"> |
| 82 <param name="fastq_input_interleaved" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> | 82 <param name="fastq_input_interleaved" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> |
| 83 </when> | 83 </when> |
| 84 </conditional> | 84 </conditional> |
| 85 | 85 |
| 86 <section name="adv" title="Advanced parameters" expanded="false"> | 86 <section name="adv" title="Advanced parameters" expanded="false"> |
| 87 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" /> | 87 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" /> |
| 146 <conditional name="reference_source"> | 146 <conditional name="reference_source"> |
| 147 <param name="reference_source_selector" value="history"/> | 147 <param name="reference_source_selector" value="history"/> |
| 148 <param name="ref_file" value="reference.fasta" ftype="fasta"/> | 148 <param name="ref_file" value="reference.fasta" ftype="fasta"/> |
| 149 </conditional> | 149 </conditional> |
| 150 <param name="fastq_input_selector" value="paired" /> | 150 <param name="fastq_input_selector" value="paired" /> |
| 151 <param name="fastq_input1" ftype="fastqsanger" value="a_1.fastq" /> | 151 <param name="fastq_input1" ftype="fastqsanger.gz" value="a_1.fastq.gz" /> |
| 152 <param name="fastq_input2" ftype="fastqsanger" value="a_2.fastq" /> | 152 <param name="fastq_input2" ftype="fastqsanger.gz" value="a_2.fastq.gz" /> |
| 153 <param name="mincov" value="2" /> | 153 <param name="mincov" value="2" /> |
| 154 <param name="minqual" value="60" /> | 154 <param name="minqual" value="60" /> |
| 155 <param name="outputs" value="outgff,outsum" /> | 155 <param name="outputs" value="outgff,outsum" /> |
| 156 <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" /> | 156 <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" /> |
| 157 <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/> | 157 <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/> |