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comparison snippy.xml @ 5:f9d3b5a6ef31 draft

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"planemo upload commit b436c43bb4e8f28c91434173f1b8cb9b187056b2"
author iuc
date Thu, 12 Sep 2019 12:42:17 -0400
parents a2147b3769dd
children eea223efd86e
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4:98413117ca70 5:f9d3b5a6ef31
1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy2"> 1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy0">
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>
7 </macros> 7 </macros>
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 10
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 12
13 #if $ref.is_of_type("fasta") 13 @REFERENCE_SOURCE_FILE@
14 cp '$ref' 'ref.fna' && 14
15 #end if
16 #if $ref.is_of_type("genbank")
17 cp '$ref' 'ref.gbk' &&
18 #end if
19 snippy 15 snippy
20 --outdir 'out' 16 --outdir 'out'
21 --cpus \${GALAXY_SLOTS:-1} 17 --cpus \${GALAXY_SLOTS:-1}
22 --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024)) 18 --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
23 #if $ref.is_of_type("fasta") 19 @REFERENCE_COMMAND@
24 --ref 'ref.fna'
25 #end if
26 #if $ref.is_of_type("genbank")
27 --ref 'ref.gbk'
28 #end if
29 --mapqual $adv.mapqual 20 --mapqual $adv.mapqual
30 --mincov $adv.mincov 21 --mincov $adv.mincov
31 --minfrac $adv.minfrac 22 --minfrac $adv.minfrac
32 --minqual $adv.minqual 23 --minqual $adv.minqual
33 #if $adv.rgid 24 #if $adv.rgid
67 #if "outcon" in str($outputs) and $adv.rename_cons 58 #if "outcon" in str($outputs) and $adv.rename_cons
68 && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa 59 && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa
69 #end if 60 #end if
70 61
71 62
72 ]]></command> 63 ]]> </command>
73 64
74 <inputs> 65 <inputs>
75 66 <expand macro="reference_selector" />
76 <param name="ref" type="data" format="fasta,genbank" label="Reference File (either in fasta or genbank format)" help="Fasta or Genbank file to use as the reference" />
77
78 <conditional name="fastq_input"> 67 <conditional name="fastq_input">
79 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> 68 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
80 <option value="paired">Paired</option> 69 <option value="paired">Paired</option>
81 <option value="single">Single</option> 70 <option value="single">Single</option>
82 <option value="paired_collection">Paired Collection</option> 71 <option value="paired_collection">Paired Collection</option>
113 <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option> 102 <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option>
114 <option value="outsum" selected="False">A summary of the samples and mapping</option> 103 <option value="outsum" selected="False">A summary of the samples and mapping</option>
115 <option value="outlog" selected="False">A log file with the commands run and their outputs</option> 104 <option value="outlog" selected="False">A log file with the commands run and their outputs</option>
116 <option value="outaln" selected="False">A version of the reference but with - at position with depth=0 and N for 0 to depth to --mincov (does not have variants)</option> 105 <option value="outaln" selected="False">A version of the reference but with - at position with depth=0 and N for 0 to depth to --mincov (does not have variants)</option>
117 <option value="outcon" selected="False">A version of the reference genome with all variants instantiated</option> 106 <option value="outcon" selected="False">A version of the reference genome with all variants instantiated</option>
118 <option value="outdep" selected="False">Output of samtools depth for the .bam file</option>
119 <option value="outbam" selected="False">The alignments in BAM format. Note that multi-mapping and unmapped reads are not present.</option> 107 <option value="outbam" selected="False">The alignments in BAM format. Note that multi-mapping and unmapped reads are not present.</option>
120 <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option> 108 <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option>
121 </param> 109 </param>
122 110
123 </inputs> 111 </inputs>
143 <filter>outputs and 'outaln' in outputs</filter> 131 <filter>outputs and 'outaln' in outputs</filter>
144 </data> 132 </data>
145 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"> 133 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
146 <filter>outputs and 'outcon' in outputs</filter> 134 <filter>outputs and 'outcon' in outputs</filter>
147 </data> 135 </data>
148 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth">
149 <filter>outputs and 'outdep' in outputs</filter>
150 </data>
151 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam"> 136 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
152 <filter>outputs and 'outbam' in outputs</filter> 137 <filter>outputs and 'outbam' in outputs</filter>
153 </data> 138 </data>
154 <data format="zip" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz"> 139 <data format="zip" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
155 <filter>outputs and 'outzip' in outputs</filter> 140 <filter>outputs and 'outzip' in outputs</filter>
157 142
158 </outputs> 143 </outputs>
159 144
160 <tests> 145 <tests>
161 146
162 <test> <!-- test 0 - fasta ref no snps --> 147 <test> <!-- test 0 - fasta ref no snps -->
163 <param name="ref" value="reference.fasta" ftype="fasta" /> 148 <!-- <param name="ref" value="reference.fasta" ftype="fasta" /> -->
149 <conditional name="reference_source">
150 <param name="reference_source_selector" value="history"/>
151 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
152 </conditional>
164 <param name="fastq_input_selector" value="paired" /> 153 <param name="fastq_input_selector" value="paired" />
165 <param name="fastq_input1" ftype="fastqsanger" value="a_1.fastq" /> 154 <param name="fastq_input1" ftype="fastqsanger" value="a_1.fastq" />
166 <param name="fastq_input2" ftype="fastqsanger" value="a_2.fastq" /> 155 <param name="fastq_input2" ftype="fastqsanger" value="a_2.fastq" />
167 <param name="mincov" value="2" /> 156 <param name="mincov" value="2" />
168 <param name="minqual" value="60" /> 157 <param name="minqual" value="60" />
169 <param name="outputs" value="outgff,outsum" /> 158 <param name="outputs" value="outgff,outsum" />
170 <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" /> 159 <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
171 <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" /> 160 <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" />
172 </test> 161 </test>
173 162
174 <test> <!-- test 1 - fasta ref one snp --> 163 <test> <!-- test 1 - fasta ref one snp -->
175 <param name="ref" value="reference.fasta" ftype="fasta" /> 164 <conditional name="reference_source">
165 <param name="reference_source_selector" value="history"/>
166 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
167 </conditional>
176 <param name="fastq_input_selector" value="paired" /> 168 <param name="fastq_input_selector" value="paired" />
177 <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" /> 169 <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" />
178 <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" /> 170 <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" />
179 <param name="mincov" value="2" /> 171 <param name="mincov" value="2" />
180 <param name="minqual" value="60" /> 172 <param name="minqual" value="60" />
181 <param name="outputs" value="outgff,outsum" /> 173 <param name="outputs" value="outgff,outsum" />
182 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" /> 174 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
183 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" /> 175 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
184 </test> 176 </test>
185 177
186 <test> <!-- test 2 - fasta ref one snp paired_collection --> 178 <test> <!-- test 2 - fasta ref one snp paired_collection -->
187 <param name="ref" value="reference.fasta" ftype="fasta" /> 179 <conditional name="reference_source">
180 <param name="reference_source_selector" value="history"/>
181 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
182 </conditional>
188 <param name="fastq_input_selector" value="paired_collection" /> 183 <param name="fastq_input_selector" value="paired_collection" />
189 <param name="fastq_input"> 184 <param name="fastq_input">
190 <collection type="paired"> 185 <collection type="paired">
191 <element name="forward" ftype="fastqsanger" value="b_1.fastq" /> 186 <element name="forward" ftype="fastqsanger" value="b_1.fastq" />
192 <element name="reverse" ftype="fastqsanger" value="b_2.fastq" /> 187 <element name="reverse" ftype="fastqsanger" value="b_2.fastq" />
197 <param name="outputs" value="outgff,outsum" /> 192 <param name="outputs" value="outgff,outsum" />
198 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" /> 193 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
199 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" /> 194 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
200 </test> 195 </test>
201 196
202 <test> <!-- test 3 - fasta ref one snp single --> 197 <test> <!-- test 3 - fasta ref one snp single -->
203 <param name="ref" value="reference.fasta" ftype="fasta" /> 198 <conditional name="reference_source">
199 <param name="reference_source_selector" value="history"/>
200 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
201 </conditional>
204 <param name="fastq_input_selector" value="single" /> 202 <param name="fastq_input_selector" value="single" />
205 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" /> 203 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
206 <param name="mincov" value="2" /> 204 <param name="mincov" value="2" />
207 <param name="minqual" value="60" /> 205 <param name="minqual" value="60" />
208 <param name="outputs" value="outgff,outsum" /> 206 <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" /> 207 <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" /> 208 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
211 </test> 209 </test>
210
211 <test> <!-- test 4 - reference source as cached -->
212 <conditional name="reference_source">
213 <param name="reference_source_selector" value="cached"/>
214 <param name="ref_file" value="test_id"/>
215 </conditional>
216 <param name="fastq_input_selector" value="single" />
217 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
218 <param name="mincov" value="2" />
219 <param name="minqual" value="60" />
220 <param name="outputs" value="outgff,outsum" />
221 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
222 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
223 </test>
212 </tests> 224 </tests>
213 225
214 226
215 <help><![CDATA[ 227 <help><![CDATA[
216 228
245 257
246 **Further information** 258 **Further information**
247 259
248 For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy 260 For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy
249 261
250 ]]></help> 262 ]]> </help>
251 <expand macro="citations"/> 263 <expand macro="citations"/>
252 264
253 </tool> 265 </tool>