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comparison snippy.xml @ 14:08d22d220254 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit bc5bbb26c53bf2455043cf4b8f552571e6f74530
author iuc
date Mon, 20 Jan 2025 10:10:04 +0000
parents fa016f1eea1a
children
comparison
equal deleted inserted replaced
13:d220115f882b 14:08d22d220254
19 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name) 19 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
20 #elif str( $fastq_input.fastq_input_selector ) == "single" 20 #elif str( $fastq_input.fastq_input_selector ) == "single"
21 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier) 21 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
22 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" 22 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
23 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier) 23 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
24 #elif str( $fastq_input.fastq_input_selector ) == "contigs"
25 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fasta_input.element_identifier)
24 #end if 26 #end if
25 27
26 snippy 28 snippy
27 --outdir '${dir_name}' 29 --outdir '${dir_name}'
28 --cpus \${GALAXY_SLOTS:-1} 30 --cpus \${GALAXY_SLOTS:-1}
47 --R2 '$fastq_input.fastq_input.reverse' 49 --R2 '$fastq_input.fastq_input.reverse'
48 #elif str( $fastq_input.fastq_input_selector ) == "single" 50 #elif str( $fastq_input.fastq_input_selector ) == "single"
49 --se '$fastq_input.fastq_input_single' 51 --se '$fastq_input.fastq_input_single'
50 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" 52 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
51 --peil '$fastq_input.fastq_input_interleaved' 53 --peil '$fastq_input.fastq_input_interleaved'
54 #elif str( $fastq_input.fastq_input_selector ) == "contigs"
55 --ctgs '$fastq_input.fasta_input'
52 #end if 56 #end if
53 57
54 #if "outcon" in str($outputs) and $adv.rename_cons 58 #if "outcon" in str($outputs) and $adv.rename_cons
55 && sed -i 's/>.*/>${dir_name}/' '${dir_name}/snps.consensus.fa' 59 && sed -i 's/>.*/>${dir_name}/' '${dir_name}/snps.consensus.fa'
56 #end if 60 #end if
60 ]]> </command> 64 ]]> </command>
61 65
62 <inputs> 66 <inputs>
63 <expand macro="reference_selector" /> 67 <expand macro="reference_selector" />
64 <conditional name="fastq_input"> 68 <conditional name="fastq_input">
65 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> 69 <param name="fastq_input_selector" type="select" label="Input type" help="Select paired/single end raw read data or assembled contigs">
66 <option value="paired">Paired</option> 70 <option value="paired">Paired end reads</option>
67 <option value="single">Single</option> 71 <option value="single">Single end reads</option>
68 <option value="paired_collection">Paired Collection</option> 72 <option value="paired_collection">Paired end reads in a collection</option>
69 <option value="paired_iv">Paired Interleaved</option> 73 <option value="paired_iv">Interleaved paired end reads</option>
74 <option value="contigs">Assembled Contigs</option>
70 </param> 75 </param>
71 <when value="paired"> 76 <when value="paired">
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"/> 77 <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,fastqsanger.gz,fasta,fasta.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/> 78 <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> 79 </when>
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"/> 84 <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> 85 </when>
81 <when value="paired_iv"> 86 <when value="paired_iv">
82 <param name="fastq_input_interleaved" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> 87 <param name="fastq_input_interleaved" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
83 </when> 88 </when>
89 <when value="contigs">
90 <param name="fasta_input" type="data" format="fasta" label="Select fasta dataset" help="Specify dataset with assembled contigs"/>
91 </when>
92
84 </conditional> 93 </conditional>
85 94
86 <section name="adv" title="Advanced parameters" expanded="false"> 95 <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" /> 96 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
88 <param name="mincov" type="integer" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" /> 97 <param name="mincov" type="integer" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />
216 <param name="minqual" value="60" /> 225 <param name="minqual" value="60" />
217 <param name="outputs" value="outgff,outsum" /> 226 <param name="outputs" value="outgff,outsum" />
218 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" /> 227 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
219 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/> 228 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
220 </test> 229 </test>
230
231 <test> <!-- test 5 - fasta ref one snp single -->
232 <conditional name="reference_source">
233 <param name="reference_source_selector" value="history"/>
234 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
235 </conditional>
236 <conditional name="fastq_input">
237 <param name="fastq_input_selector" value="contigs" />
238 <param name="fasta_input" value="contigs.fasta" ftype="fasta" />
239 </conditional>
240 <param name="mincov" value="2" />
241 <param name="minqual" value="60" />
242 <param name="outputs" value="outgff,outsum" />
243 <output name="snpsum" ftype="tabular" file="d_fna_ref_mincov_1_minqual_60.snps.txt" lines_diff="6" />
244 <output name="snpgff" ftype="gff3" file="d_fna_ref_mincov_1_minqual_60.snps.gff" lines_diff="2"/>
245 </test>
221 </tests> 246 </tests>
222 247
223 248
224 <help><![CDATA[ 249 <help><![CDATA[
225 250