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comparison meryl.xml @ 7:51c2360aa807 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8"
author iuc
date Mon, 28 Jun 2021 09:32:16 +0000
parents 31fa26c0692b
children 5ae3496f9ca3
comparison
equal deleted inserted replaced
6:31fa26c0692b 7:51c2360aa807
1 <tool id='meryl' name='Meryl' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'> 1 <tool id='meryl' name='Meryl' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@' profile='20.01'>
2 <description>a genomic k-mer counter and sequence utility</description> 2 <description>a genomic k-mer counter and sequence utility</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro='edam_ontology' /> 6 <expand macro='edam_ontology' />
151 <param name="count_operations" type="select" label="Count operations" help="Select an operation to be executed"> 151 <param name="count_operations" type="select" label="Count operations" help="Select an operation to be executed">
152 <option value="count">Count: count the occurrences of canonical k-mers</option> 152 <option value="count">Count: count the occurrences of canonical k-mers</option>
153 <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option> 153 <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option>
154 <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option> 154 <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option>
155 </param> 155 </param>
156 <param name="input_reads" type="data" format="fastq,fasta" label="Input sequences" help="Select your reads in FASTA/FASTQ format." /> 156 <param name="input_reads" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Input sequences" help="Select your reads in FASTA/FASTQ format." />
157 <conditional name="options_kmer_size"> 157 <conditional name="options_kmer_size">
158 <param name="kmer_size" type="select" label="K-mer size selector"> 158 <param name="kmer_size" type="select" label="K-mer size selector">
159 <option value="provide">Set a k-mer size</option> 159 <option value="provide">Set a k-mer size</option>
160 <option value="estimate">Estimate the best k-mer size</option> 160 <option value="estimate">Estimate the best k-mer size</option>
161 </param> 161 </param>
223 </when> 223 </when>
224 <when value="print"> 224 <when value="print">
225 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" /> 225 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" />
226 </when> 226 </when>
227 <when value="trio-mode"> 227 <when value="trio-mode">
228 <param name="child_reads" type="data" format="fastq,fasta" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly" /> 228 <param name="child_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly" />
229 <param name="paternal_reads" type="data" format="fastq,fasta" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly" /> 229 <param name="paternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly" />
230 <param name="maternal_reads" type="data" format="fastq,fasta" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly" /> 230 <param name="maternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly" />
231 <conditional name="options_kmer_size"> 231 <conditional name="options_kmer_size">
232 <param name="kmer_size" type="select" label="K-mer size selector"> 232 <param name="kmer_size" type="select" label="K-mer size selector">
233 <option value="provide">Set a k-mer size</option> 233 <option value="provide">Set a k-mer size</option>
234 <option value="estimate">Estimate the best k-mer size</option> 234 <option value="estimate">Estimate the best k-mer size</option>
235 </param> 235 </param>
425 <assert_contents> 425 <assert_contents>
426 <has_size value="56100" delta="300" /> 426 <has_size value="56100" delta="300" />
427 </assert_contents> 427 </assert_contents>
428 </output> 428 </output>
429 </test> 429 </test>
430 <!-- test 11 --> 430 <!-- test 12 -->
431 <test expect_num_outputs="1"> 431 <test expect_num_outputs="1">
432 <conditional name="operation_type"> 432 <conditional name="operation_type">
433 <param name="command_type" value="arithmetic-kmers" /> 433 <param name="command_type" value="arithmetic-kmers" />
434 <param name="arithmetic_operations" value="modulo" /> 434 <param name="arithmetic_operations" value="modulo" />
435 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" /> 435 <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
436 <param name="X" value="3" /> 436 <param name="X" value="3" />
437 </conditional> 437 </conditional>
438 <output name="read_db" ftype="meryldb"> 438 <output name="read_db" ftype="meryldb">
439 <assert_contents> 439 <assert_contents>
440 <has_size value="37172" delta="300" /> 440 <has_size value="37501" delta="300" />
441 </assert_contents> 441 </assert_contents>
442 </output> 442 </output>
443 </test> 443 </test>
444 <test expect_num_outputs="1"> 444 <test expect_num_outputs="1">
445 <conditional name="operation_type"> 445 <conditional name="operation_type">
616 <conditional name="operation_type"> 616 <conditional name="operation_type">
617 <param name="command_type" value="print" /> 617 <param name="command_type" value="print" />
618 <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" /> 618 <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" />
619 </conditional> 619 </conditional>
620 <output name="read_db_print" file="output_25.read-db.tabular" sort="True"/> 620 <output name="read_db_print" file="output_25.read-db.tabular" sort="True"/>
621 </test>
622 <!--Test compressed files-->
623 <test expect_num_outputs="1">
624 <conditional name="operation_type">
625 <param name="command_type" value="count-kmers" />
626 <param name="count_operation" value="count" />
627 <param name="input_reads" value="child.fasta.gz" />
628 <conditional name="options_kmer_size">
629 <param name="kmer_size" value="provide" />
630 <param name="input_kmer_size" value="7" />
631 </conditional>
632 </conditional>
633 <output name="read_db" ftype="meryldb">
634 <assert_contents>
635 <has_size value="1851" delta="300" />
636 </assert_contents>
637 </output>
638 <assert_stdout>
639 <has_line line="K-mer size: 7" />
640 </assert_stdout>
621 </test> 641 </test>
622 </tests> 642 </tests>
623 <help><![CDATA[ 643 <help><![CDATA[
624 644
625 .. class:: infomark 645 .. class:: infomark