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comparison canu.xml @ 4:86f150c8019d draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 9e1d3a4dcabeec3c52e08372753d32d684dbed59"
author bgruening
date Wed, 03 Nov 2021 16:10:37 +0000
parents 5732f959936a
children
comparison
equal deleted inserted replaced
3:5732f959936a 4:86f150c8019d
2 <description>Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore</description> 2 <description>Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore</description>
3 <xrefs> 3 <xrefs>
4 <xref type="bio.tools">canu</xref> 4 <xref type="bio.tools">canu</xref>
5 </xrefs> 5 </xrefs>
6 <macros> 6 <macros>
7 <token name="@TOOL_VERSION@">2.1.1</token> 7 <token name="@TOOL_VERSION@">2.2</token>
8 <token name="@VERSION_SUFFIX@">0</token> 8 <token name="@VERSION_SUFFIX@">0</token>
9 </macros> 9 </macros>
10 <requirements> 10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">canu</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">canu</requirement>
12 </requirements> 12 </requirements>
40 minOverlapLength=$minOverlapLength 40 minOverlapLength=$minOverlapLength
41 corOutCoverage=$corOutCoverage 41 corOutCoverage=$corOutCoverage
42 #if $stopOnLowCoverage 42 #if $stopOnLowCoverage
43 stopOnLowCoverage=$stopOnLowCoverage 43 stopOnLowCoverage=$stopOnLowCoverage
44 #end if 44 #end if
45 #if $minInputCoverage 45 #if $minInputCoverage ##and $stage in ["all", "trim-assemble", "assemble"]
46 minInputCoverage=$minInputCoverage 46 minInputCoverage=$minInputCoverage
47 #end if 47 #end if
48 contigFilter=' 48 contigFilter='
49 ${contigFilter.minReads} 49 ${contigFilter.minReads}
50 ${contigFilter.minLength} 50 ${contigFilter.minLength}
54 ' 54 '
55 55
56 genomeSize='$genomeSize' 56 genomeSize='$genomeSize'
57 minThreads=\${GALAXY_SLOTS:-4} 57 minThreads=\${GALAXY_SLOTS:-4}
58 maxThreads=\${GALAXY_SLOTS:-4} 58 maxThreads=\${GALAXY_SLOTS:-4}
59 redMemory=\${GALAXY_MEMORY_MB:-4096}M 59 redMemory=\${GALAXY_MEMORY_MB:-6144}M
60 redThreads=\${GALAXY_SLOTS:-4} 60 redThreads=\${GALAXY_SLOTS:-4}
61 obtovlThreads=\${GALAXY_SLOTS:-4} 61 obtovlThreads=\${GALAXY_SLOTS:-4}
62 utgovlThreads=\${GALAXY_SLOTS:-4} 62 utgovlThreads=\${GALAXY_SLOTS:-4}
63 batThreads=\${GALAXY_SLOTS:-4} 63 batThreads=\${GALAXY_SLOTS:-4}
64 batMemory=\${GALAXY_MEMORY_MB:-4096}M 64 batMemory=\${GALAXY_MEMORY_MB:-6144}M
65 cormhapMemory=\${GALAXY_MEMORY_MB:-4096}M 65 cormhapMemory=\${GALAXY_MEMORY_MB:-6144}M
66 obtovlMemory=\${GALAXY_MEMORY_MB:-4096}M 66 obtovlMemory=\${GALAXY_MEMORY_MB:-6144}M
67 utgovlMemory=\${GALAXY_MEMORY_MB:-4096}M 67 utgovlMemory=\${GALAXY_MEMORY_MB:-6144}M
68 corThreads=\${GALAXY_SLOTS:-4} 68 corThreads=\${GALAXY_SLOTS:-4}
69 corMemory=\${GALAXY_MEMORY_MB:-4096}M 69 corMemory=\${GALAXY_MEMORY_MB:-6144}M
70 cnsThreads=\${GALAXY_SLOTS:-4} 70 cnsThreads=\${GALAXY_SLOTS:-4}
71 cnsMemory=\${GALAXY_MEMORY_MB:-4096}M 71 cnsMemory=\${GALAXY_MEMORY_MB:-6144}M
72 oeaMemory=\${GALAXY_MEMORY_MB:-4096}M 72 oeaMemory=\${GALAXY_MEMORY_MB:-6144}M
73 oeaThreads=\${GALAXY_SLOTS:-4} 73 oeaThreads=\${GALAXY_SLOTS:-4}
74 merylThreads=\${GALAXY_SLOTS:-4}
75 merylMemory=\${GALAXY_MEMORY_MB:-6144}M
76 corovlThreads=\${GALAXY_SLOTS:-4}
77 corovlMemory=\${GALAXY_MEMORY_MB:-6144}M
74 useGrid=false 78 useGrid=false
75 79
76 #for $haplotype in $haplotypes: 80 #for $haplotype in $haplotypes:
77 -haplotype${haplotype.haplotype_name} '${haplotype.haplotype_input}' 81 -haplotype${haplotype.haplotype_name} '${haplotype.haplotype_input}'
78 #end for 82 #end for
163 <output name="unassembled" ftype="fasta" file="ecoli_canu_unassembled_result1.fa"/> 167 <output name="unassembled" ftype="fasta" file="ecoli_canu_unassembled_result1.fa"/>
164 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result1.fa.gz"/> 168 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result1.fa.gz"/>
165 <output name="trimmed_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_trimmed_reads_result1.fa.gz"/> 169 <output name="trimmed_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_trimmed_reads_result1.fa.gz"/>
166 <output name="report"> 170 <output name="report">
167 <assert_contents> 171 <assert_contents>
168 <has_n_lines n="488"/> 172 <has_n_lines n="486"/>
169 <has_text_matching expression="[UNITIGGING/CONTIGS]"/> 173 <has_text_matching expression="[UNITIGGING/CONTIGS]"/>
170 <has_text_matching expression="-- Contig sizes based on genome size 20kbp:"/> 174 <has_text_matching expression="-- Contig sizes based on genome size 20kbp:"/>
171 </assert_contents> 175 </assert_contents>
172 </output> 176 </output>
173 </test> 177 </test>
186 <output name="unassembled" ftype="fasta" file="ecoli_canu_unassembled_result2.fa"/> 190 <output name="unassembled" ftype="fasta" file="ecoli_canu_unassembled_result2.fa"/>
187 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result2.fa.gz"/> 191 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result2.fa.gz"/>
188 <output name="trimmed_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_trimmed_reads_result2.fa.gz"/> 192 <output name="trimmed_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_trimmed_reads_result2.fa.gz"/>
189 <output name="report"> 193 <output name="report">
190 <assert_contents> 194 <assert_contents>
191 <has_n_lines n="464"/> 195 <has_n_lines n="456"/>
192 <has_text_matching expression="[UNITIGGING/CONTIGS]"/> 196 <has_text_matching expression="[UNITIGGING/CONTIGS]"/>
193 <has_text_matching expression="-- Contig sizes based on genome size 20kbp:"/> 197 <has_text_matching expression="-- Contig sizes based on genome size 20kbp:"/>
194 </assert_contents> 198 </assert_contents>
195 </output> 199 </output>
196 </test> 200 </test>
202 <param name="stopOnLowCoverage" value="1"/> 206 <param name="stopOnLowCoverage" value="1"/>
203 <param name="minReadLength" value="2500"/> 207 <param name="minReadLength" value="2500"/>
204 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result3.fa.gz"/> 208 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result3.fa.gz"/>
205 <output name="report"> 209 <output name="report">
206 <assert_contents> 210 <assert_contents>
207 <has_n_lines n="187"/> 211 <has_n_lines n="189"/>
208 <has_text_matching expression="[TRIMMING/READS]"/> 212 <has_text_matching expression="[TRIMMING/READS]"/>
209 <has_text_matching expression="-- Found 89 reads."/> 213 <has_text_matching expression="-- Found 93 reads."/>
210 </assert_contents> 214 </assert_contents>
211 </output> 215 </output>
212 </test> 216 </test>
213 <!--trimming test - it does currently not trim anything due to the input data --> 217 <!--trimming test - it does currently not trim anything due to the input data -->
214 <test expect_num_outputs="2"> 218 <test expect_num_outputs="2">
215 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/> 219 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/>
216 <param name="technology" value="-nanopore"/> 220 <param name="technology" value="-nanopore"/>
217 <param name="genomeSize" value="3.4m"/> 221 <param name="processing" value="-corrected"/>
222 <!-- <param name="minInputCoverage" value="1"/> -->
223 <param name="genomeSize" value="0.01m"/>
218 <param name="stage" value="-trim"/> 224 <param name="stage" value="-trim"/>
219 <param name="minReadLength" value="500"/> 225 <param name="minReadLength" value="500"/>
220 <output name="report"> 226 <output name="report">
221 <assert_contents> 227 <assert_contents>
222 <has_text_matching expression="[TRIMMING/READS]"/> 228 <has_text_matching expression="[TRIMMING/READS]"/>
223 <has_n_lines n="6"/> 229 <has_n_lines n="209"/>
224 <has_text_matching expression="Found 0 reads."/> 230 <has_text_matching expression="Found 112 reads."/><!-- before trimming -->
231 <has_text_matching expression="Found 61 reads."/><!-- after trimming -->
225 </assert_contents> 232 </assert_contents>
226 </output> 233 </output>
227 </test> 234 </test>
228 <!--test expect_num_outputs="5"> 235 <!--test expect_num_outputs="5">
229 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/> 236 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/>