Mercurial > repos > iuc > snapatac2_preprocessing

comparison preprocessing.xml @ 1:e3b85e48487b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
author iuc
date Wed, 17 Jul 2024 05:54:26 +0000
parents b2844c6efb72
children 3d1103801ff2
comparison
equal deleted inserted replaced
0:b2844c6efb72 1:e3b85e48487b
83 min_frag_size = $method.min_frag_size, 83 min_frag_size = $method.min_frag_size,
84 #end if 84 #end if
85 #if $method.max_frag_size 85 #if $method.max_frag_size
86 max_frag_size = $method.max_frag_size, 86 max_frag_size = $method.max_frag_size,
87 #end if 87 #end if
88 ##counting_strategy = '$method.counting_strategy', 88 counting_strategy = '$method.counting_strategy',
89 count_frag_as_reads = $method.count_frag_as_reads,
90 n_jobs = int(os.getenv("GALAXY_SLOTS", 4)) 89 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
91 ) 90 )
92 91
93 #else if $method.method == 'pp.make_gene_matrix' 92 #else if $method.method == 'pp.make_gene_matrix'
94 adata = sa.pp.make_gene_matrix( 93 adata = sa.pp.make_gene_matrix(
105 min_frag_size = $method.min_frag_size, 104 min_frag_size = $method.min_frag_size,
106 #end if 105 #end if
107 #if $method.max_frag_size 106 #if $method.max_frag_size
108 max_frag_size = $method.max_frag_size, 107 max_frag_size = $method.max_frag_size,
109 #end if 108 #end if
110 ##counting_strategy = '$method.counting_strategy' 109 counting_strategy = '$method.counting_strategy'
111 count_frag_as_reads = $method.count_frag_as_reads
112 ) 110 )
113 111
114 #else if $method.method == 'pp.filter_cells' 112 #else if $method.method == 'pp.filter_cells'
115 sa.pp.filter_cells( 113 sa.pp.filter_cells(
116 adata, 114 adata,
283 <expand macro="param_chunk_size" size="500"/> 281 <expand macro="param_chunk_size" size="500"/>
284 <param argument="exclude_chroms" type="text" value="chrM, chrY, M, Y" optional="true" label="A list of chromosomes to exclude"> 282 <param argument="exclude_chroms" type="text" value="chrM, chrY, M, Y" optional="true" label="A list of chromosomes to exclude">
285 <expand macro="sanitize_query"/> 283 <expand macro="sanitize_query"/>
286 </param> 284 </param>
287 <expand macro="min_max_frag_size"/> 285 <expand macro="min_max_frag_size"/>
288 <!--expand macro="param_counting_strategy"/--> 286 <expand macro="param_counting_strategy"/>
289 <param argument="count_frag_as_reads" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to count fragments as reads"/>
290 </when> 287 </when>
291 <when value="pp.make_gene_matrix"> 288 <when value="pp.make_gene_matrix">
292 <expand macro="inputs_anndata"/> 289 <expand macro="inputs_anndata"/>
293 <param argument="gene_anno" type="data" format="gtf,gff3" label="GTF/GFF file containing the gene annotation"/> 290 <param argument="gene_anno" type="data" format="gtf,gff3" label="GTF/GFF file containing the gene annotation"/>
294 <expand macro="param_chunk_size" size="500"/> 291 <expand macro="param_chunk_size" size="500"/>
300 <param argument="transcript_name_key" type="text" value="transcript_name" label="The key of the transcript name in the gene annotation file"/> 297 <param argument="transcript_name_key" type="text" value="transcript_name" label="The key of the transcript name in the gene annotation file"/>
301 <param argument="transcript_id_key" type="text" value="transcript_id" label="The key of the transcript id in the gene annotation file"/> 298 <param argument="transcript_id_key" type="text" value="transcript_id" label="The key of the transcript id in the gene annotation file"/>
302 <param argument="gene_name_key" type="text" value="gene_name" label="The key of the gene name in the gene annotation file"/> 299 <param argument="gene_name_key" type="text" value="gene_name" label="The key of the gene name in the gene annotation file"/>
303 <param argument="gene_id_key" type="text" value="gene_id" label="The key of the gene id in the gene annotation file"/> 300 <param argument="gene_id_key" type="text" value="gene_id" label="The key of the gene id in the gene annotation file"/>
304 <expand macro="min_max_frag_size"/> 301 <expand macro="min_max_frag_size"/>
305 <!--expand macro="param_counting_strategy"/--> 302 <expand macro="param_counting_strategy"/>
306 <param argument="count_frag_as_reads" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to count fragments as reads"/>
307 </when> 303 </when>
308 <when value="pp.filter_cells"> 304 <when value="pp.filter_cells">
309 <expand macro="inputs_anndata"/> 305 <expand macro="inputs_anndata"/>
310 <param argument="min_counts" type="integer" value="1000" label="Minimum number of counts required for a cell to pass filtering"/> 306 <param argument="min_counts" type="integer" value="1000" label="Minimum number of counts required for a cell to pass filtering"/>
311 <param argument="min_tsse" type="float" value="5.0" label="Minimum TSS enrichemnt score required for a cell to pass filtering"/> 307 <param argument="min_tsse" type="float" value="5.0" label="Minimum TSS enrichemnt score required for a cell to pass filtering"/>
444 <param name="id_type" value="gene"/> 440 <param name="id_type" value="gene"/>
445 <param name="transcript_name_key" value="transcript_name"/> 441 <param name="transcript_name_key" value="transcript_name"/>
446 <param name="transcript_id_key" value="transcript_id"/> 442 <param name="transcript_id_key" value="transcript_id"/>
447 <param name="gene_name_key" value="gene_name"/> 443 <param name="gene_name_key" value="gene_name"/>
448 <param name="gene_id_key" value="gene_id"/> 444 <param name="gene_id_key" value="gene_id"/>
449 <param name="count_frag_as_reads" value="True"/> 445 <param name="counting_strategy" value="insertion"/>
450 </conditional> 446 </conditional>
451 <section name="advanced_common"> 447 <section name="advanced_common">
452 <param name="show_log" value="true" /> 448 <param name="show_log" value="true" />
453 </section> 449 </section>
454 <output name="hidden_output"> 450 <output name="hidden_output">
459 <has_text_matching expression="id_type = 'gene'"/> 455 <has_text_matching expression="id_type = 'gene'"/>
460 <has_text_matching expression="transcript_name_key = 'transcript_name'"/> 456 <has_text_matching expression="transcript_name_key = 'transcript_name'"/>
461 <has_text_matching expression="transcript_id_key = 'transcript_id'"/> 457 <has_text_matching expression="transcript_id_key = 'transcript_id'"/>
462 <has_text_matching expression="gene_name_key = 'gene_name'"/> 458 <has_text_matching expression="gene_name_key = 'gene_name'"/>
463 <has_text_matching expression="gene_id_key = 'gene_id'"/> 459 <has_text_matching expression="gene_id_key = 'gene_id'"/>
464 <has_text_matching expression="count_frag_as_reads = True"/> 460 <has_text_matching expression="counting_strategy = 'insertion'"/>
465 </assert_contents> 461 </assert_contents>
466 </output> 462 </output>
467 <output name="anndata_out" location="https://zenodo.org/records/12548681/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" /> 463 <output name="anndata_out" location="https://zenodo.org/records/12548681/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
468 </test> 464 </test>
469 <test expect_num_outputs="2"> 465 <test expect_num_outputs="2">
511 <param name="method" value="pp.add_tile_matrix"/> 507 <param name="method" value="pp.add_tile_matrix"/>
512 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad"/> 508 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
513 <param name="bin_size" value="5000"/> 509 <param name="bin_size" value="5000"/>
514 <param name="chunk_size" value="500"/> 510 <param name="chunk_size" value="500"/>
515 <param name="exclude_chroms" value="chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr22, chrX, chrY"/> 511 <param name="exclude_chroms" value="chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr22, chrX, chrY"/>
516 <param name="count_frag_as_reads" value="True"/> 512 <param name="counting_strategy" value="insertion"/>
517 </conditional> 513 </conditional>
518 <section name="advanced_common"> 514 <section name="advanced_common">
519 <param name="show_log" value="true" /> 515 <param name="show_log" value="true" />
520 </section> 516 </section>
521 <output name="hidden_output"> 517 <output name="hidden_output">
522 <assert_contents> 518 <assert_contents>
523 <has_text_matching expression="sa.pp.add_tile_matrix"/> 519 <has_text_matching expression="sa.pp.add_tile_matrix"/>
524 <has_text_matching expression="bin_size = 5000"/> 520 <has_text_matching expression="bin_size = 5000"/>
525 <has_text_matching expression="chunk_size = 500"/> 521 <has_text_matching expression="chunk_size = 500"/>
526 <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/> 522 <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
527 <has_text_matching expression="count_frag_as_reads = True"/> 523 <has_text_matching expression="counting_strategy = 'insertion'"/>
524 </assert_contents>
525 </output>
526 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/>
527 </test>
528 <test expect_num_outputs="2">
529 <!-- pp.add_tile_matrix counting_strategy fragment -->
530 <conditional name="method">
531 <param name="method" value="pp.add_tile_matrix"/>
532 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
533 <param name="bin_size" value="5000"/>
534 <param name="chunk_size" value="500"/>
535 <param name="exclude_chroms" value="chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr22, chrX, chrY"/>
536 <param name="counting_strategy" value="fragment"/>
537 </conditional>
538 <section name="advanced_common">
539 <param name="show_log" value="true" />
540 </section>
541 <output name="hidden_output">
542 <assert_contents>
543 <has_text_matching expression="sa.pp.add_tile_matrix"/>
544 <has_text_matching expression="bin_size = 5000"/>
545 <has_text_matching expression="chunk_size = 500"/>
546 <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
547 <has_text_matching expression="counting_strategy = 'fragment'"/>
528 </assert_contents> 548 </assert_contents>
529 </output> 549 </output>
530 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/> 550 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/>
531 </test> 551 </test>
532 <test expect_num_outputs="2"> 552 <test expect_num_outputs="2">