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comparison coverm_genome.xml @ 1:a671907f96fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
author iuc
date Tue, 24 Jan 2023 12:32:54 +0000
parents 134e4e78e754
children 5bf5792b0996
comparison
equal deleted inserted replaced
0:134e4e78e754 1:a671907f96fe
1 <tool id="coverm_genome" name="CoverM-GENOME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> 1 <tool id="coverm_genome" name="CoverM genome" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>read coverage and relative abundance calculator focused on metagenomics applications</description> 2 <description>Calculate coverage of individual genomes</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command><![CDATA[ 7 <command><![CDATA[
133 #set $fname = $input_file.element_identifier.replace(" ","_") 133 #set $fname = $input_file.element_identifier.replace(" ","_")
134 #set $file_path = 'reference/' + $fname 134 #set $file_path = 'reference/' + $fname
135 ln -s '$input_file' '$file_path' && 135 ln -s '$input_file' '$file_path' &&
136 $ref_files.append($file_path) 136 $ref_files.append($file_path)
137 #end for 137 #end for
138 #if $reads.genome.add_genome.add_genome 138 #if $reads.genome.add_genome.add_genome == "true"
139 mkdir -p genomes && 139 mkdir -p genomes &&
140 #set genome_files = [] 140 #set genome_files = []
141 #if $reads.genome.add_genome.add_genomic == "history" 141 #if $reads.genome.add_genome.add_genomic == "history"
142 #for $input_file in $reads.genome.add_genome.add_genomic.fasta_history 142 #for $input_file in $reads.genome.add_genome.add_genomic.fasta_history
143 #set $fname = $input_file.element_identifier.replace(" ","_") 143 #set $fname = $input_file.element_identifier.replace(" ","_")
154 $genome_files.append($file_path) 154 $genome_files.append($file_path)
155 #end for 155 #end for
156 #end if 156 #end if
157 #end if 157 #end if
158 #end if 158 #end if
159 159
160 mkdir ./representative-fasta/ &&
160 coverm genome 161 coverm genome
161 #if $reads.read_type == 'paired' 162 #if $reads.read_type == 'paired'
162 -1 163 -1
163 #for $read in $fw_reads1 164 #for $read in $fw_reads1
164 '${read}' 165 '${read}'
238 #else 239 #else
239 #if $reads.genome.cond_single_genome.separator 240 #if $reads.genome.cond_single_genome.separator
240 -s "$reads.genome.cond_single_genome.separator" 241 -s "$reads.genome.cond_single_genome.separator"
241 #end if 242 #end if
242 #end if 243 #end if
243 #if $reads.genome.add_genome.add_genome 244 #if $reads.genome.add_genome.add_genome == "true"
244 -f 245 -f
245 #for $genome in $genome_files 246 #for $genome in $genome_files
246 '${genome}' 247 '${genome}'
247 #end for 248 #end for
248 #end if 249 #end if
253 $reads.genome.single_genome 254 $reads.genome.single_genome
254 #end if 255 #end if
255 256
256 $derep.dereplicate 257 $derep.dereplicate
257 #if $derep.checkm_tab_table: 258 #if $derep.checkm_tab_table:
258 --chekm-tab-table $derep.checkm_tab_table 259 --chekm-tab-table '$derep.checkm_tab_table'
259 #end if 260 #end if
260 #if $derep.genome_info: 261 #if $derep.genome_info:
261 --genome-info $derep.genome_info 262 --genome-info '$derep.genome_info'
262 #end if 263 #end if
263 #if $derep.min_completeness: 264 #if $derep.min_completeness != "":
264 --min-completeness $derep.min_completeness 265 --min-completeness $derep.min_completeness
265 #end if 266 #end if
266 #if $derep.max_contamination: 267 #if $derep.max_contamination != "":
267 --max-contamination $derep.max_contamination 268 --max-contamination $derep.max_contamination
268 #end if 269 #end if
269 #if $derep.dereplication_ani: 270 #if $derep.dereplication_ani != "":
270 --dereplication-ani $derep.dereplication_ani 271 --dereplication-ani $derep.dereplication_ani
271 #end if 272 #end if
272 #if $derep.dereplication_aligned_fraction: 273 #if $derep.dereplication_aligned_fraction != "":
273 --dereplication-aligned-fraction $derep.dereplication_aligned_fraction 274 --dereplication-aligned-fraction $derep.dereplication_aligned_fraction
274 #end if 275 #end if
275 #if $derep.dereplication_fragment_length: 276 #if $derep.dereplication_fragment_length != "":
276 --dereplication-fragment-length $derep.dereplication_fragment_length 277 --dereplication-fragment-length $derep.dereplication_fragment_length
277 #end if 278 #end if
278 #if $derep.dereplication_prethreshold_ani: 279 #if $derep.dereplication_prethreshold_ani != "":
279 --dereplication-prethreshold-ani $derep.dereplication_prethreshold_ani 280 --dereplication-prethreshold-ani $derep.dereplication_prethreshold_ani
280 #end if 281 #end if
281 #if $derep.dereplication_quality_formula: 282 #if $derep.dereplication_quality_formula:
282 --dereplication-quality-formula $derep.dereplication_quality_formula 283 --dereplication-quality-formula $derep.dereplication_quality_formula
283 #end if 284 #end if
313 $mapping.exclude_supplementary 314 $mapping.exclude_supplementary
314 315
315 --methods $cov.relative_abundance $cov.mean $cov.cond_methods.trimmed_mean $cov.covered_bases $cov.covered_fraction 316 --methods $cov.relative_abundance $cov.mean $cov.cond_methods.trimmed_mean $cov.covered_bases $cov.covered_fraction
316 $cov.variance $cov.length $cov.count $cov.metabat $cov.coverage_histogram $cov.reads_per_base 317 $cov.variance $cov.length $cov.count $cov.metabat $cov.coverage_histogram $cov.reads_per_base
317 $cov.rpkm $cov.tpm 318 $cov.rpkm $cov.tpm
318 #if $cov.min_covered_fraction: 319 #if $cov.min_covered_fraction != "":
319 --min-covered-fraction $cov.min_covered_fraction 320 --min-covered-fraction $cov.min_covered_fraction
320 #end if 321 #end if
321 #if $cov.contig_end_exclusion: 322 #if $cov.contig_end_exclusion != "":
322 --contig-end-exclusion $cov.contig_end_exclusion 323 --contig-end-exclusion $cov.contig_end_exclusion
323 #end if 324 #end if
324 #if $cov.cond_methods.trimmed_mean 325 #if $cov.cond_methods.trimmed_mean == "trimmed_mean"
325 #if $cov.cond_methods.trim_min: 326 #if $cov.cond_methods.trim_min:
326 --trim-min $cov.cond_methods.trim_min 327 --trim-min $cov.cond_methods.trim_min
327 #end if 328 #end if
328 #if $cov.cond_methods.trim_max: 329 #if $cov.cond_methods.trim_max:
329 --trim_max $cov.cond_methods.trim_max 330 --trim_max $cov.cond_methods.trim_max
332 333
333 #if $out.output_format: 334 #if $out.output_format:
334 --output-format $out.output_format 335 --output-format $out.output_format
335 #end if 336 #end if
336 #if $out.dereplication_output_cluster_definition: 337 #if $out.dereplication_output_cluster_definition:
337 --dereplication-output-cluster-definition 338 --dereplication-output-cluster-definition '$cluster_definition'
338 #end if 339 #end if
339 #if $out.dereplication_output_representative_fasta_directory_copy: 340 #if $out.dereplication_output_representative_fasta_directory_copy:
340 --dereplication-output-representative-fasta-directory-copy . 341 --dereplication-output-representative-fasta-directory-copy ./representative-fasta/
341 #end if 342 #end if
342 $out.no_zeros 343 $out.no_zeros
343 --output-file output.tsv 344 --output-file output.tsv
344 --threads \${GALAXY_SLOTS:-1} 345 --threads \${GALAXY_SLOTS:-1}
345 2> stdout.txt 346
347 #if $derep.dereplicate and $out.dereplication_output_cluster_definition
348 && sed -i -e 's@genomes/@@g; s/\.fna//g' '$cluster_definition'
349 #end if
346 ]]></command> 350 ]]></command>
347 <inputs> 351 <inputs>
348 <expand macro="reads" /> 352 <expand macro="reads" />
349 <expand macro="add_reads" /> 353 <expand macro="add_reads" />
350 <section name="derep" title="Dereplication options" expanded="false"> 354 <section name="derep" title="Dereplication options" expanded="false">
392 <expand macro="coverage"/> 396 <expand macro="coverage"/>
393 <expand macro="out"/> 397 <expand macro="out"/>
394 </inputs> 398 </inputs>
395 <outputs> 399 <outputs>
396 <data name="output1" format="tsv" from_work_dir="./output.tsv"/> 400 <data name="output1" format="tsv" from_work_dir="./output.tsv"/>
397 <data name="cluster-definition" format="tsv"> 401 <data name="cluster_definition" format="tsv" label="${tool.name} on ${on_string}: cluster definition">
398 <filter>out['dereplication_output_cluster_definition']</filter> 402 <filter>derep['dereplicate'] and out['dereplication_output_cluster_definition']</filter>
399 </data> 403 </data>
404 <collection name="representative_fasta" type="list" label="${tool.name} on ${on_string}: representative fasta">
405 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fna" format="fasta" directory="representative-fasta" />
406 <filter>derep['dereplicate'] and out['dereplication_output_representative_fasta_directory_copy']</filter>
407 </collection>
400 </outputs> 408 </outputs>
401 <tests> 409 <tests>
402 <test> 410 <test expect_num_outputs="1">
403 <conditional name="reads"> 411 <conditional name="reads">
404 <param name="read_type" value="paired_collection"/> 412 <param name="read_type" value="paired_collection"/>
405 <param name="paired_reads"> 413 <param name="paired_reads">
406 <collection type="list:paired"> 414 <collection type="list:paired">
407 <element name="reads_for_seq1_and_seq2..fq"> 415 <element name="reads_for_seq1_and_seq2..fq">
487 <assert_contents> 495 <assert_contents>
488 <has_n_lines n="2"/> 496 <has_n_lines n="2"/>
489 </assert_contents> 497 </assert_contents>
490 </output> 498 </output>
491 </test> 499 </test>
492 <test expect_num_outputs="1"> 500 <test expect_num_outputs="3">
493 <conditional name="reads"> 501 <conditional name="reads">
494 <param name="read_type" value="paired_collection"/> 502 <param name="read_type" value="paired_collection"/>
495 <param name="paired_reads"> 503 <param name="paired_reads">
496 <collection type="list:paired"> 504 <collection type="list:paired">
497 <element name="reads_for_genome2"> 505 <element name="reads_for_genome2">
511 </conditional> 519 </conditional>
512 </conditional> 520 </conditional>
513 <section name="cov"> 521 <section name="cov">
514 <param name="mean" value="true"/> 522 <param name="mean" value="true"/>
515 </section> 523 </section>
524 <section name="derep">
525 <param name="dereplicate" value="true"/>
526 </section>
527 <section name="out">
528 <param name="dereplication_output_cluster_definition" value="true"/>
529 <param name="dereplication_output_representative_fasta_directory_copy" value="true"/>
530 </section>
516 <output name="output1" file="test3.tsv" ftype="tsv"/> 531 <output name="output1" file="test3.tsv" ftype="tsv"/>
532 <output name="cluster_definition" ftype="tsv" value="test4_cluster.tsv"/>
533 <output_collection name="representative_fasta" type="list" count="3">
534 <element name="genome1" file="test4_rep1.fa" ftype="fasta" />
535 <element name="genome2" file="test4_rep2.fa" ftype="fasta" />
536 <element name="genome3" file="test4_rep3.fa" ftype="fasta" />
537 </output_collection>
517 </test> 538 </test>
518 <test expect_num_outputs="1"> 539 <test expect_num_outputs="1">
519 <conditional name="reads"> 540 <conditional name="reads">
520 <param name="read_type" value="bam"/> 541 <param name="read_type" value="bam"/>
521 <param name="bam" value="2seqs.bad_read.1.with_supplementary.bam"/> 542 <param name="bam" value="2seqs.bad_read.1.with_supplementary.bam"/>