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comparison abyss-pe.xml @ 19:38c11e3dde7f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit c083399ddb31b026aaab1d600d8789bf56cf4d4b
author iuc
date Mon, 18 Sep 2023 11:04:10 +0000
parents f58d3e818ebc
children dd49135a0c3b
comparison
equal deleted inserted replaced
18:f58d3e818ebc 19:38c11e3dde7f
1 <tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>de novo sequence assembler</description> 2 <description>de novo sequence assembler</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.3.6</token> 4 <token name="@TOOL_VERSION@">2.3.6</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 <xml name="reads_conditional"> 6 <xml name="reads_conditional">
7 <conditional name="reads"> 7 <conditional name="reads">
8 <param name="reads_selector" type="select" label="Type of paired-end datasets"> 8 <param name="reads_selector" type="select" label="Type of paired-end datasets">
9 <option value="paired">2 separate datasets</option> 9 <option value="paired">2 separate datasets</option>
10 <option value="paired_collection">1 paired dataset collection</option> 10 <option value="paired_collection">1 paired dataset collection</option>
83 #end if 83 #end if
84 84
85 abyss-pe 85 abyss-pe
86 name=abyss 86 name=abyss
87 j=\${GALAXY_SLOTS:-1} 87 j=\${GALAXY_SLOTS:-1}
88 B=\${GALAXY_MEMORY_MB:-2048}M 88 B=\$((\${GALAXY_MEMORY_MB:-2048} * 9 /10 ))M
89
89 k=$k 90 k=$k
90 91
91 #if str($K) 92 #if str($K)
92 K=$K 93 K=$K
93 #end if 94 #end if
225 <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" /> 226 <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" />
226 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" /> 227 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" />
227 </outputs> 228 </outputs>
228 229
229 <tests> 230 <tests>
230 <test> 231 <test expect_num_outputs="5">
231 <repeat name="lib_repeat"> 232 <repeat name="lib_repeat">
232 <conditional name="reads"> 233 <conditional name="reads">
233 <param name="reads_selector" value="paired" /> 234 <param name="reads_selector" value="paired" />
234 <param name="reads1" ftype="fastqsanger.gz" value="assembly_sample-R1.fastq.gz" /> 235 <param name="reads1" ftype="fastqsanger.gz" value="assembly_sample-R1.fastq.gz" />
235 <param name="reads2" ftype="fastqsanger.gz" value="assembly_sample-R2.fastq.gz" /> 236 <param name="reads2" ftype="fastqsanger.gz" value="assembly_sample-R2.fastq.gz" />
240 <output name="contigs_outfile" file="abyss-contigs1.fa" /> 241 <output name="contigs_outfile" file="abyss-contigs1.fa" />
241 <output name="scaffolds" file="abyss-scaffolds1.fa" /> 242 <output name="scaffolds" file="abyss-scaffolds1.fa" />
242 <output name="indels" file="empty_file.fasta" /> 243 <output name="indels" file="empty_file.fasta" />
243 <output name="stats" file="abyss-stats1.tab" /> 244 <output name="stats" file="abyss-stats1.tab" />
244 </test> 245 </test>
245 <test> 246 <test expect_num_outputs="3">
246 <param name="se_reads" ftype="fastq.gz" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" /> 247 <param name="se_reads" ftype="fastq.gz" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
247 <param name="k" value="50" /> 248 <param name="k" value="50" />
248 <output name="unitigs" file="abyss-unitigs2.fa" /> 249 <output name="unitigs" file="abyss-unitigs2.fa" />
249 <output name="indels" file="empty_file.fasta" /> 250 <output name="indels" file="empty_file.fasta" />
250 <output name="stats" file="abyss-stats2.tab" /> 251 <output name="stats" file="abyss-stats2.tab" />
251 </test> 252 </test>
252 <test> 253 <test expect_num_outputs="4">
253 <param name="se_reads" ftype="fasta" value="assembly_sample-R1.fasta,assembly_sample-R2.fasta" /> 254 <param name="se_reads" ftype="fasta" value="assembly_sample-R1.fasta,assembly_sample-R2.fasta" />
254 <param name="long_seqs" ftype="fasta" value="assembly_sample-R2.fasta" /> 255 <param name="long_seqs" ftype="fasta" value="assembly_sample-R2.fasta" />
255 <param name="k" value="50" /> 256 <param name="k" value="50" />
256 <output name="unitigs" file="abyss-unitigs3.fa" /> 257 <output name="unitigs" file="abyss-unitigs3.fa" />
257 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" /> 258 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />