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comparison snippy.xml @ 12:fa016f1eea1a draft

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"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
comparison
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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"/>