Mercurial > repos > iuc > snapatac2_preprocessing

comparison preprocessing.xml @ 2:48d9421bf176 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
author iuc
date Fri, 05 Jul 2024 11:06:01 +0000
parents cec3e76eaf05
children 4ecdea4cbea1
comparison
equal deleted inserted replaced
1:cec3e76eaf05 2:48d9421bf176
89 count_frag_as_reads = $method.count_frag_as_reads, 89 count_frag_as_reads = $method.count_frag_as_reads,
90 n_jobs = int(os.getenv("GALAXY_SLOTS", 4)) 90 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
91 ) 91 )
92 92
93 #else if $method.method == 'pp.make_gene_matrix' 93 #else if $method.method == 'pp.make_gene_matrix'
94 sa.pp.make_gene_matrix( 94 adata = sa.pp.make_gene_matrix(
95 adata, 95 adata,
96 gene_anno = '$method.gene_anno', 96 gene_anno = '$method.gene_anno',
97 chunk_size = $method.chunk_size, 97 chunk_size = $method.chunk_size,
98 use_x = $method.use_x, 98 use_x = $method.use_x,
99 id_type = '$method.id_type', 99 id_type = '$method.id_type',
462 <has_text_matching expression="gene_name_key = 'gene_name'"/> 462 <has_text_matching expression="gene_name_key = 'gene_name'"/>
463 <has_text_matching expression="gene_id_key = 'gene_id'"/> 463 <has_text_matching expression="gene_id_key = 'gene_id'"/>
464 <has_text_matching expression="count_frag_as_reads = True"/> 464 <has_text_matching expression="count_frag_as_reads = True"/>
465 </assert_contents> 465 </assert_contents>
466 </output> 466 </output>
467 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" /> 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" />
468 </test> 468 </test>
469 <test expect_num_outputs="2"> 469 <test expect_num_outputs="2">
470 <!-- metrics.tsse --> 470 <!-- metrics.tsse -->
471 <conditional name="method"> 471 <conditional name="method">
472 <param name="method" value="metrics.tsse"/> 472 <param name="method" value="metrics.tsse"/>