snapatac2_preprocessing: preprocessing.xml annotate

annotate preprocessing.xml @ 3:3d1103801ff2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit a9dc6c2d00d4488dfb751609bac74b19f241e06a

author	iuc
date	Thu, 07 Nov 2024 13:07:30 +0000
parents	e3b85e48487b
children	20d723aaa07c

rev	line source
0 b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	1 <tool id="snapatac2_preprocessing" name="SnapATAC2 Preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	2 <description>and integration</description>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	3 <macros>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	4 <import>macros.xml</import>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	5 </macros>
3 3d1103801ff2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit a9dc6c2d00d4488dfb751609bac74b19f241e06a iuc parents: 1 diff changeset	6 <expand macro="xrefs"/>
0 b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	7 <requirements>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	8 <expand macro="requirements"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	9 </requirements>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	10 <command detect_errors="exit_code"><![CDATA[
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	11 #if $method.method != 'pp.make_fragment_file' and $method.method != 'pp.import_data'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	12 @PREP_ADATA@
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	13 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	14 @CMD@
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	15 ]]></command>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	16 <configfiles>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	17 <configfile name="script_file"><![CDATA[
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	18 @CMD_imports@
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	19
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	20 #if $method.method != 'pp.make_fragment_file' and $method.method != 'pp.import_data'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	21 @CMD_read_inputs@
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	22 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	23
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	24 #if $method.method == 'pp.make_fragment_file'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	25 sa.pp.make_fragment_file(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	26 bam_file = '$method.bam_file',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	27 is_paired = $method.is_paired,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	28 #if $method.barcode.extract_type == 'from_tag'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	29 #if $method.barcode.barcode_tag != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	30 barcode_tag = '$method.barcode.barcode_tag',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	31 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	32 #elif $method.barcode.extract_type == 'from_read_names'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	33 #if $method.barcode.barcode_regex != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	34 barcode_regex = '$method.barcode.barcode_regex',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	35 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	36 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	37 #if $method.umi_tag != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	38 umi_tag = '$method.umi_tag',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	39 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	40 #if $method.umi_regex != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	41 umi_regex = '$method.umi_regex',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	42 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	43 shift_right = $method.shift_right,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	44 shift_left = $method.shift_left,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	45 min_mapq = $method.min_mapq,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	46 chunk_size = $method.chunk_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	47 compression = 'gzip',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	48 output_file = '$fragments_out',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	49 tempdir = "."
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	50 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	51
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	52 #else if $method.method == 'pp.import_data'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	53 import csv
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	54 with open('$method.chrom_sizes') as f:
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	55 chr_sizes = {x[0]:int(x[1]) for x in csv.reader(f, delimiter='\t')}
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	56
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	57 sa.pp.import_data(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	58 fragment_file = '$method.fragment_file',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	59 chrom_sizes = chr_sizes,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	60 min_num_fragments = $method.min_num_fragments,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	61 sorted_by_barcode = $method.sorted_by_barcode,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	62 #if str($method.whitelist) != 'None'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	63 whitelist = '$method.whitelist',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	64 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	65 shift_left = $method.shift_left,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	66 shift_right = $method.shift_right,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	67 #set $chr_mt = ([x.strip() for x in str($method.chrM).split(',')])
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	68 chrM = $chr_mt,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	69 chunk_size = $method.chunk_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	70 file = 'anndata.h5ad',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	71 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	72 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	73
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	74 #else if $method.method == 'pp.add_tile_matrix'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	75 sa.pp.add_tile_matrix(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	76 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	77 bin_size = $method.bin_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	78 chunk_size = $method.chunk_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	79 #if $method.exclude_chroms != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	80 #set $excl_chroms = ([x.strip() for x in str($method.exclude_chroms).split(',')])
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	81 exclude_chroms = $excl_chroms,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	82 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	83 #if $method.min_frag_size
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	84 min_frag_size = $method.min_frag_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	85 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	86 #if $method.max_frag_size
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	87 max_frag_size = $method.max_frag_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	88 #end if
1 e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	89 counting_strategy = '$method.counting_strategy',
0 b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	90 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	91 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	92
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	93 #else if $method.method == 'pp.make_gene_matrix'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	94 adata = sa.pp.make_gene_matrix(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	95 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	96 gene_anno = '$method.gene_anno',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	97 chunk_size = $method.chunk_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	98 use_x = $method.use_x,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	99 id_type = '$method.id_type',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	100 transcript_name_key = '$method.transcript_name_key',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	101 transcript_id_key = '$method.transcript_id_key',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	102 gene_name_key = '$method.gene_name_key',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	103 gene_id_key = '$method.gene_id_key',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	104 #if $method.min_frag_size
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	105 min_frag_size = $method.min_frag_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	106 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	107 #if $method.max_frag_size
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	108 max_frag_size = $method.max_frag_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	109 #end if
1 e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	110 counting_strategy = '$method.counting_strategy'
0 b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	111 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	112
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	113 #else if $method.method == 'pp.filter_cells'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	114 sa.pp.filter_cells(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	115 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	116 min_counts = $method.min_counts,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	117 min_tsse = $method.min_tsse,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	118 #if $method.max_counts
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	119 max_counts = $method.max_counts,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	120 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	121 #if $method.max_tsse
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	122 max_tsse = $method.max_tsse,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	123 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	124 inplace = True,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	125 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	126 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	127
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	128 #else if $method.method == 'pp.select_features'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	129 sa.pp.select_features(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	130 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	131 n_features = $method.n_features,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	132 filter_lower_quantile = $method.filter_lower_quantile,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	133 filter_upper_quantile = $method.filter_upper_quantile,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	134 #if str($method.whitelist) != 'None'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	135 whitelist = '$method.whitelist',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	136 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	137 #if str($method.blacklist) != 'None'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	138 blacklist = '$method.blacklist',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	139 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	140 max_iter = $method.max_iter,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	141 inplace = True,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	142 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	143 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	144
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	145 #else if $method.method == 'pp.scrublet'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	146 sa.pp.scrublet(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	147 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	148 #if $method.features
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	149 features = '$method.features',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	150 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	151 n_comps = $method.n_comps,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	152 sim_doublet_ratio = $method.sim_doublet_ratio,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	153 expected_doublet_rate = $method.expected_doublet_rate,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	154 #if $method.n_neighbors
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	155 n_neighbors = $method.n_neighbors,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	156 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	157 use_approx_neighbors = $method.use_approx_neighbors,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	158 random_state = $method.random_state,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	159 inplace = True,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	160 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	161 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	162
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	163 #else if $method.method == 'pp.filter_doublets'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	164 sa.pp.filter_doublets(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	165 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	166 #if $method.probability_threshold
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	167 probability_threshold = $method.probability_threshold,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	168 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	169 #if $method.score_threshold
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	170 score_threshold = $method.score_threshold,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	171 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	172 inplace = True,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	173 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	174 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	175
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	176 #else if $method.method == 'pp.mnc_correct'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	177 sa.pp.mnc_correct(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	178 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	179 batch = '$method.batch',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	180 n_neighbors = $method.n_neighbors,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	181 n_clusters = $method.n_clusters,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	182 n_iter = $method.n_iter,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	183 @CMD_params_data_integration@
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	184 inplace = True,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	185 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	186 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	187
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	188 #else if $method.method == 'pp.harmony'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	189 sa.pp.harmony(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	190 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	191 batch = '$method.batch',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	192 @CMD_params_data_integration@
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	193 inplace = True
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	194 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	195
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	196 #else if $method.method == 'pp.scanorama_integrate'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	197 sa.pp.scanorama_integrate(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	198 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	199 batch = '$method.batch',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	200 n_neighbors = $method.n_neighbors,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	201 @CMD_params_data_integration@
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	202 inplace = True
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	203 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	204
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	205 #else if $method.method == 'metrics.frag_size_distr'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	206 sa.metrics.frag_size_distr(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	207 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	208 max_recorded_size = $method.max_recorded_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	209 add_key = '$method.add_key',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	210 inplace = True,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	211 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	212 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	213
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	214 #else if $method.method == 'metrics.tsse'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	215 sa.metrics.tsse(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	216 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	217 gene_anno = '$method.gene_anno',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	218 inplace = True,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	219 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	220 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	221 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	222
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	223 #if $method.method != 'pp.make_fragment_file' and $method.method != 'pp.import_data'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	224 @CMD_anndata_write_outputs@
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	225 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	226 ]]></configfile>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	227 </configfiles>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	228 <inputs>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	229 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	230 <param name="method" type="select" label="Method used for preprocessing">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	231 <option value="pp.make_fragment_file">Convert a BAM file to a fragment file, using 'pp.make_fragment_file'</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	232 <option value="pp.import_data">Import data fragment files and compute basic QC metrics, using 'pp.import_data'</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	233 <option value="pp.add_tile_matrix">Generate cell by bin count matrix, using 'pp.add_tile_matrix'</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	234 <option value="pp.make_gene_matrix">Generate cell by gene activity matrix, using 'pp.make_gene_matrix'</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	235 <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using 'pp.filter_cells'</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	236 <option value="pp.select_features">Perform feature selection, using 'pp.select_features'</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	237 <option value="pp.scrublet">Compute probability of being a doublet using the scrublet algorithm, using 'pp.scrublet'</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	238 <option value="pp.filter_doublets">Remove doublets according to the doublet probability or doublet score, using 'pp.filter_doublets'</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	239 <option value="pp.mnc_correct">A modified MNN-Correct algorithm based on cluster centroid, using 'pp.mnc_correct'</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	240 <option value="pp.harmony">Use harmonypy to integrate different experiments,using 'pp.harmony'</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	241 <option value="pp.scanorama_integrate">Use Scanorama [Hie19] to integrate different experiments, using 'pp.scanorama_integrate'</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	242 <option value="metrics.frag_size_distr">Compute the fragment size distribution of the dataset, using 'metrics.frag_size_distr'</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	243 <option value="metrics.tsse">Compute the TSS enrichment score (TSSe) for each cell, using 'metrics.tsse'</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	244 </param>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	245 <when value="pp.make_fragment_file">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	246 <param argument="bam_file" type="data" format="bam" label="File name of the BAM file"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	247 <param argument="is_paired" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Indicate whether the BAM file contain paired-end reads"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	248 <conditional name="barcode">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	249 <param name="extract_type" type="select" label="How to extract barcodes from BAM records?">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	250 <option value="from_tag">From TAG fileds</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	251 <option value="from_read_names">From read names using regular expressions</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	252 </param>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	253 <when value="from_tag">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	254 <param argument="barcode_tag" type="text" value="CB" optional="true" label="Extract barcodes from TAG fields of BAM records"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	255 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	256 <when value="from_read_names">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	257 <param argument="barcode_regex" type="text" value="" optional="true" label="Extract barcodes from read names of BAM records using regular expressions" help="`(..:..:..:..):\w+$` extracts `bd:69:Y6:10` from `A01535:24:HW2MMDSX2:2:1359:8513:3458:bd:69:Y6:10:TGATAGGTT``"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	258 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	259 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	260 <param argument="umi_tag" type="text" value="" optional="true" label="Extract UMI from TAG fields of BAM records"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	261 <param argument="umi_regex" type="text" value="" optional="true" label="Extract UMI from read names of BAM records using regular expressions"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	262 <expand macro="param_shift"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	263 <param argument="min_mapq" type="integer" min="0" value="30" label="Filter the reads based on MAPQ"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	264 <expand macro="param_chunk_size" size="50000000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	265 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	266 <when value="pp.import_data">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	267 <param argument="fragment_file" type="data" format="interval" label="Fragment file, optionally compressed with gzip or zstd"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	268 <param argument="chrom_sizes" type="data" format="tabular" label="A tabular file containing chromosome names and sizes"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	269 <param argument="min_num_fragments" type="integer" value="200" label="Number of unique fragments threshold used to filter cells"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	270 <param argument="sorted_by_barcode" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether the fragment file has been sorted by cell barcodes"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	271 <param argument="whitelist" type="data" format="txt" optional="True" label="Whitelist file with a list of barcodes" help="Each line must contain a valid barcode. When provided, only barcodes in the whitelist will be retained."/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	272 <param argument="chrM" type="text" value="chrM, M" label="A list of chromosome names that are considered mitochondrial DNA">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	273 <expand macro="sanitize_query"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	274 </param>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	275 <param argument="shift_left" type="integer" value="0" label="Insertion site correction for the left end" help="Note this has no effect on single-end reads"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	276 <param argument="shift_right" type="integer" value="0" label="Insertion site correction for the right end" help="Note this has no effect on single-end reads"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	277 <expand macro="param_chunk_size" size="2000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	278 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	279 <when value="pp.add_tile_matrix">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	280 <expand macro="inputs_anndata"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	281 <param argument="bin_size" type="integer" value="500" label="The size of consecutive genomic regions used to record the counts"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	282 <expand macro="param_chunk_size" size="500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	283 <param argument="exclude_chroms" type="text" value="chrM, chrY, M, Y" optional="true" label="A list of chromosomes to exclude">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	284 <expand macro="sanitize_query"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	285 </param>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	286 <expand macro="min_max_frag_size"/>
1 e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	287 <expand macro="param_counting_strategy"/>
0 b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	288 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	289 <when value="pp.make_gene_matrix">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	290 <expand macro="inputs_anndata"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	291 <param argument="gene_anno" type="data" format="gtf,gff3" label="GTF/GFF file containing the gene annotation"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	292 <expand macro="param_chunk_size" size="500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	293 <param argument="use_x" type="boolean" truevalue="True" falsevalue="False" checked="false" label="If True, use the matrix stored in .X as raw counts"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	294 <param argument="id_type" type="select" label="Id type, 'gene' or 'transcript'">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	295 <option value="gene" selected="true">gene</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	296 <option value="transcript">transcript</option>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	297 </param>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	298 <param argument="transcript_name_key" type="text" value="transcript_name" label="The key of the transcript name in the gene annotation file"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	299 <param argument="transcript_id_key" type="text" value="transcript_id" label="The key of the transcript id in the gene annotation file"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	300 <param argument="gene_name_key" type="text" value="gene_name" label="The key of the gene name in the gene annotation file"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	301 <param argument="gene_id_key" type="text" value="gene_id" label="The key of the gene id in the gene annotation file"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	302 <expand macro="min_max_frag_size"/>
1 e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	303 <expand macro="param_counting_strategy"/>
0 b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	304 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	305 <when value="pp.filter_cells">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	306 <expand macro="inputs_anndata"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	307 <param argument="min_counts" type="integer" value="1000" label="Minimum number of counts required for a cell to pass filtering"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	308 <param argument="min_tsse" type="float" value="5.0" label="Minimum TSS enrichemnt score required for a cell to pass filtering"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	309 <param argument="max_counts" type="integer" value="" optional="true" label="Maximum number of counts required for a cell to pass filtering"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	310 <param argument="max_tsse" type="float" value="" optional="true" label="Maximum TSS enrichment score expressed required for a cell to pass filtering"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	311 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	312 <when value="pp.select_features">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	313 <expand macro="inputs_anndata"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	314 <param argument="n_features" type="integer" min="1" value="500000" label="Number of features to keep"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	315 <param argument="filter_lower_quantile" type="float" min="0" value="0.005" label="Lower quantile of the feature count distribution to filter out"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	316 <param argument="filter_upper_quantile" type="float" min="0" value="0.005" label="Upper quantile of the feature count distribution to filter out"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	317 <param argument="whitelist" type="data" format="bed" optional="true" label="A user provided bed file containing genome-wide whitelist regions"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	318 <param argument="blacklist" type="data" format="bed" optional="true" label="A user provided bed file containing genome-wide blacklist regions"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	319 <param argument="max_iter" type="integer" value="1" label="If greater than 1, this function will perform iterative clustering and feature selection"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	320 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	321 <when value="pp.scrublet">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	322 <expand macro="inputs_anndata"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	323 <param argument="features" type="text" value="" optional="true" label=" Boolean index mask, where True means that the feature is kept, and False means the feature is removed."/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	324 <param argument="n_comps" type="integer" value="15" label="Number of components" help="15 is usually sufficient. The algorithm is not sensitive to this parameter"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	325 <param argument="sim_doublet_ratio" type="float" value="2.0" label="Number of doublets to simulate relative to the number of observed cells"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	326 <param argument="expected_doublet_rate" type="float" value="0.1" label="Expected doublet rate"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	327 <param argument="n_neighbors" type="integer" value="" optional="true" label="Number of neighbors used to construct the KNN graph of observed cells and simulated doublets"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	328 <param argument="use_approx_neighbors" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Whether to use approximate search"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	329 <param argument="random_state" type="integer" value="0" label="Random state"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	330 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	331 <when value="pp.filter_doublets">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	332 <expand macro="inputs_anndata"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	333 <param argument="probability_threshold" type="float" value="0.5" label="Threshold for doublet probability"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	334 <param argument="score_threshold" type="float" value="" optional="true" label="Threshold for doublet score"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	335 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	336 <when value="pp.mnc_correct">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	337 <expand macro="inputs_anndata"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	338 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	339 <expand macro="sanitize_query"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	340 </param>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	341 <param argument="n_neighbors" type="integer" value="5" label="Number of mutual nearest neighbors"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	342 <param argument="n_clusters" type="integer" value="40" label="Number of clusters"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	343 <param argument="n_iter" type="integer" value="1" label="Number of iterations"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	344 <expand macro="params_data_integration"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	345 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	346 <when value="pp.harmony">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	347 <expand macro="inputs_anndata"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	348 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	349 <expand macro="sanitize_query"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	350 </param>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	351 <expand macro="params_data_integration"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	352 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	353 <when value="pp.scanorama_integrate">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	354 <expand macro="inputs_anndata"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	355 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	356 <expand macro="sanitize_query"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	357 </param>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	358 <param argument="n_neighbors" type="integer" value="20" label="Number of mutual nearest neighbors"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	359 <expand macro="params_data_integration"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	360 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	361 <when value="metrics.frag_size_distr">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	362 <!-- TODO move this to plotting -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	363 <expand macro="inputs_anndata"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	364 <param argument="max_recorded_size" type="integer" min="1" value="1000" label="The maximum fragment size to record in the result"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	365 <param argument="add_key" type="text" value="frag_size_distr" label="Key used to store the result in `adata.uns`"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	366 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	367 <when value="metrics.tsse">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	368 <!-- TODO move this to plotting -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	369 <expand macro="inputs_anndata"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	370 <param argument="gene_anno" type="data" format="gtf,gff3" label="GTF/GFF file containing the gene annotation"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	371 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	372 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	373 <expand macro="inputs_common_advanced"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	374 </inputs>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	375 <outputs>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	376 <data name="fragments_out" format="interval" label="${tool.name} (${method.method}) on ${on_string}: Fragment file">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	377 <filter>method['method'] == 'pp.make_fragment_file'</filter>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	378 </data>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	379 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	380 <filter>method['method'] != 'pp.make_fragment_file'</filter>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	381 </data>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	382 <data name="hidden_output" format="txt" label="Log file">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	383 <filter>advanced_common['show_log']</filter>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	384 </data>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	385 </outputs>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	386 <tests>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	387 <test expect_num_outputs="1">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	388 <!-- pp.make_fragment_file -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	389 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	390 <param name="method" value="pp.make_fragment_file"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	391 <param name="bam_file" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21_subsample.bam"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	392 <param name="is_paired" value="true"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	393 <conditional name="barcode">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	394 <param name="extract_type" value="from_tag"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	395 <param name="barcode_tag" value="CB"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	396 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	397 <param name="shift_left" value="4"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	398 <param name="shift_right" value="-5"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	399 <param name="min_mapq" value="10"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	400 <param name="chunk_size" value="50000000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	401 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	402 <output name="fragments_out" location="https://zenodo.org/records/11260316/files/pp.make_fragment_file.pbmc_500_chr21.tsv.gz" ftype="interval" compare="sim_size" delta_frac="0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	403 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	404 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	405 <!-- pp.pp.import_data -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	406 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	407 <param name="method" value="pp.import_data"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	408 <param name="fragment_file" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21.tsv.gz"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	409 <param name="chrom_sizes" location="https://zenodo.org/records/11260316/files/chr21_size.tabular"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	410 <param name="min_num_fragments" value="1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	411 <param name="sorted_by_barcode" value="False"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	412 <param name="shift_left" value="0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	413 <param name="chrM" value="chrM, M"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	414 <param name="shift_right" value="0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	415 <param name="chunk_size" value="1000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	416 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	417 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	418 <param name="show_log" value="true"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	419 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	420 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	421 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	422 <has_text_matching expression="sa.pp.import_data"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	423 <has_text_matching expression="min_num_fragments = 1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	424 <has_text_matching expression="sorted_by_barcode = False"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	425 <has_text_matching expression="shift_left = 0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	426 <has_text_matching expression="chrM = \['chrM', 'M'\]"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	427 <has_text_matching expression="shift_right = 0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	428 <has_text_matching expression="chunk_size = 1000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	429 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	430 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	431 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	432 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	433 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	434 <!-- pp.make_gene_matrix -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	435 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	436 <param name="method" value="pp.make_gene_matrix"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	437 <param name="adata" location="https://zenodo.org/records/11260316/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	438 <param name="gene_anno" location="https://zenodo.org/records/11260316/files/chr21.gff3.gz"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	439 <param name="chunk_size" value="500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	440 <param name="use_x" value="False"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	441 <param name="id_type" value="gene"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	442 <param name="transcript_name_key" value="transcript_name"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	443 <param name="transcript_id_key" value="transcript_id"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	444 <param name="gene_name_key" value="gene_name"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	445 <param name="gene_id_key" value="gene_id"/>
1 e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	446 <param name="counting_strategy" value="insertion"/>
0 b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	447 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	448 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	449 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	450 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	451 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	452 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	453 <has_text_matching expression="sa.pp.make_gene_matrix"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	454 <has_text_matching expression="chunk_size = 500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	455 <has_text_matching expression="use_x = False"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	456 <has_text_matching expression="id_type = 'gene'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	457 <has_text_matching expression="transcript_name_key = 'transcript_name'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	458 <has_text_matching expression="transcript_id_key = 'transcript_id'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	459 <has_text_matching expression="gene_name_key = 'gene_name'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	460 <has_text_matching expression="gene_id_key = 'gene_id'"/>
1 e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	461 <has_text_matching expression="counting_strategy = 'insertion'"/>
0 b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	462 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	463 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	464 <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" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	465 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	466 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	467 <!-- metrics.tsse -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	468 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	469 <param name="method" value="metrics.tsse"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	470 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	471 <param name="gene_anno" location="https://zenodo.org/records/11260316/files/chr21.gff3.gz"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	472 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	473 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	474 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	475 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	476 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	477 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	478 <has_text_matching expression="sa.metrics.tsse"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	479 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	480 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	481 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	482 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	483 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	484 <!-- pp.filter_cells -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	485 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	486 <param name="method" value="pp.filter_cells"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	487 <param name="adata" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	488 <param name="min_counts" value="200"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	489 <param name="min_tsse" value="5"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	490 <param name="max_counts" value="10000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	491 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	492 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	493 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	494 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	495 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	496 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	497 <has_text_matching expression="sa.pp.filter_cells"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	498 <has_text_matching expression="min_counts = 200"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	499 <has_text_matching expression="min_tsse = 5"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	500 <has_text_matching expression="max_counts = 10000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	501 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	502 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	503 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	504 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	505 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	506 <!-- pp.add_tile_matrix -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	507 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	508 <param name="method" value="pp.add_tile_matrix"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	509 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	510 <param name="bin_size" value="5000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	511 <param name="chunk_size" value="500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	512 <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"/>
1 e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	513 <param name="counting_strategy" value="insertion"/>
0 b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	514 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	515 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	516 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	517 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	518 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	519 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	520 <has_text_matching expression="sa.pp.add_tile_matrix"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	521 <has_text_matching expression="bin_size = 5000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	522 <has_text_matching expression="chunk_size = 500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	523 <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
1 e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	524 <has_text_matching expression="counting_strategy = 'insertion'"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	525 </assert_contents>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	526 </output>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	527 <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"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	528 </test>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	529 <test expect_num_outputs="2">
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	530 <!-- pp.add_tile_matrix counting_strategy fragment -->
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	531 <conditional name="method">
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	532 <param name="method" value="pp.add_tile_matrix"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	533 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	534 <param name="bin_size" value="5000"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	535 <param name="chunk_size" value="500"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	536 <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"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	537 <param name="counting_strategy" value="fragment"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	538 </conditional>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	539 <section name="advanced_common">
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	540 <param name="show_log" value="true" />
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	541 </section>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	542 <output name="hidden_output">
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	543 <assert_contents>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	544 <has_text_matching expression="sa.pp.add_tile_matrix"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	545 <has_text_matching expression="bin_size = 5000"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	546 <has_text_matching expression="chunk_size = 500"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	547 <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984 iuc parents: 0 diff changeset	548 <has_text_matching expression="counting_strategy = 'fragment'"/>
0 b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	549 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	550 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	551 <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"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	552 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	553 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	554 <!-- pp.select_features -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	555 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	556 <param name="method" value="pp.select_features"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	557 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	558 <param name="n_features" value="15000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	559 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	560 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	561 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	562 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	563 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	564 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	565 <has_text_matching expression="sa.pp.select_features"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	566 <has_text_matching expression="n_features = 15000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	567 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	568 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	569 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.select_features.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	570 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	571 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	572 <!-- pp.scrublet -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	573 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	574 <param name="method" value="pp.scrublet"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	575 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.select_features.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	576 <param name="n_comps" value="15"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	577 <param name="sim_doublet_ratio" value="2.0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	578 <param name="expected_doublet_rate" value="0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	579 <param name="random_state" value="0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	580 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	581 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	582 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	583 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	584 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	585 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	586 <has_text_matching expression="sa.pp.scrublet"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	587 <has_text_matching expression="n_comps = 15"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	588 <has_text_matching expression="sim_doublet_ratio = 2.0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	589 <has_text_matching expression="expected_doublet_rate = 0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	590 <has_text_matching expression="random_state = 0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	591 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	592 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	593 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.scrublet.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	594 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	595 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	596 <!-- pp.filter_doublets -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	597 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	598 <param name="method" value="pp.filter_doublets"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	599 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.scrublet.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	600 <param name="probability_threshold" value="0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	601 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	602 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	603 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	604 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	605 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	606 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	607 <has_text_matching expression="sa.pp.filter_doublets"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	608 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	609 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	610 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.filter_doublets.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	611 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	612 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	613 <!-- pp.mnc_correct -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	614 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	615 <param name="method" value="pp.mnc_correct"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	616 <param name="adata" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21.batch.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	617 <param name="batch" value="batch"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	618 <param name="n_neighbors" value="3"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	619 <param name="n_clusters" value="10"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	620 <param name="use_rep" value="X_spectral"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	621 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	622 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	623 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	624 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	625 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	626 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	627 <has_text_matching expression="sa.pp.mnc_correct"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	628 <has_text_matching expression="batch = 'batch'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	629 <has_text_matching expression="n_neighbors = 3"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	630 <has_text_matching expression="n_clusters = 10"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	631 <has_text_matching expression="batch = 'batch'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	632 <has_text_matching expression="use_rep = 'X_spectral'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	633 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	634 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	635 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.mnc_correct.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	636 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	637 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	638 <!-- pp.harmony -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	639 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	640 <param name="method" value="pp.harmony"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	641 <param name="adata" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21.batch.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	642 <param name="batch" value="batch"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	643 <param name="use_rep" value="X_spectral"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	644 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	645 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	646 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	647 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	648 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	649 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	650 <has_text_matching expression="sa.pp.harmony"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	651 <has_text_matching expression="batch = 'batch'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	652 <has_text_matching expression="use_rep = 'X_spectral'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	653 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	654 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	655 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.harmony.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	656 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	657 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	658 <!-- pp.scanorama_integrate -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	659 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	660 <param name="method" value="pp.scanorama_integrate"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	661 <param name="adata" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21.batch.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	662 <param name="batch" value="batch"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	663 <param name="use_rep" value="X_spectral"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	664 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	665 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	666 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	667 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	668 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	669 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	670 <has_text_matching expression="sa.pp.scanorama_integrate"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	671 <has_text_matching expression="batch = 'batch'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	672 <has_text_matching expression="use_rep = 'X_spectral'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	673 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	674 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	675 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.scanorama_integrate.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	676 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	677 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	678 <!-- metrics.frag_size_distr -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	679 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	680 <param name="method" value="metrics.frag_size_distr"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	681 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	682 <param name="max_recorded_size" value="500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	683 <param name="add_key" value="frag_size_distr"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	684 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	685 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	686 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	687 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	688 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	689 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	690 <has_text_matching expression="sa.metrics.frag_size_distr"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	691 <has_text_matching expression="add_key = 'frag_size_distr'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	692 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	693 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	694 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/metrics.frag_size_distr.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	695 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	696 </tests>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	697 <help><![CDATA[
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	698 Convert a BAM file`to a fragment file, using `pp.make_fragment_file`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	699 ====================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	700
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	701 Convert a BAM file to a fragment file.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	702
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	703 Convert a BAM file to a fragment file by performing the following steps:
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	704
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	705 - Filtering: remove reads that are unmapped, not primary alignment, mapq < 30, fails platform/vendor quality checks, or optical duplicate. For paired-end sequencing, it also removes reads that are not properly aligned.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	706
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	707 - Deduplicate: Sort the reads by cell barcodes and remove duplicated reads for each unique cell barcode.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	708
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	709 - Output: Convert BAM records to fragments (if paired-end) or single-end reads.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	710
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	711 The bam file needn’t be sorted or filtered.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	712
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	713 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	714 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.make_fragment_file.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	715
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	716 Import data fragment file` and compute basic QC metrics, using `pp.import_data`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	717 ===============================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	718
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	719 Import data fragment files and compute basic QC metrics.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	720
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	721 A fragment refers to the sequence data originating from a distinct location in the genome. In single-ended sequencing, one read equates to a fragment. However, in paired-ended sequencing, a fragment is defined by a pair of reads. This function is designed to handle, store, and process input files with fragment data, further yielding a range of basic Quality Control (QC) metrics. These metrics include the total number of unique fragments, duplication rates, and the percentage of mitochondrial DNA detected.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	722
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	723 How fragments are stored is dependent on the sequencing approach utilized. For single-ended sequencing, fragments are found in `.obsm['fragment_single']`. In contrast, for paired-ended sequencing, they are located in `.obsm['fragment_paired']`.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	724
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	725 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	726 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.import_data.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	727
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	728 Generate cell by bin count matrix, using `pp.add_tile_matrix`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	729 =============================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	730
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	731 Generate cell by bin count matrix.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	732
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	733 This function is used to generate and add a cell by bin count matrix to the AnnData object.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	734
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	735 `import_data` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	736
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	737 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	738 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.add_tile_matrix.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	739
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	740 Generate cell by gene activity matrix, using `pp.make_gene_matrix`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	741 ==================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	742
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	743 Generate cell by gene activity matrix.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	744
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	745 Generate cell by gene activity matrix by counting the TN5 insertions in gene body regions. The result will be stored in a new file and a new AnnData object will be created.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	746
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	747 `import_data` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	748
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	749 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	750 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.make_gene_matrix.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	751
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	752 Filter cell outliers based on counts and numbers of genes expressed, using `pp.filter_cells`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	753 ============================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	754
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	755 Filter cell outliers based on counts and numbers of genes expressed. For instance, only keep cells with at least `min_counts` counts or `min_ts`` TSS enrichment scores. This is to filter measurement outliers, i.e. “unreliable” observations.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	756
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	757 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	758 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.filter_cells.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	759
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	760 Perform feature selection, using `pp.select_features`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	761 =====================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	762
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	763 Perform feature selection by selecting the most accessibile features across all cells unless `max_iter` > 1
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	764
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	765 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	766 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.select_features.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	767
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	768 Compute probability of being a doublet using the scrublet algorithm, using `pp.scrublet`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	769 ========================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	770
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	771 Compute probability of being a doublet using the scrublet algorithm.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	772
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	773 This function identifies doublets by generating simulated doublets using randomly pairing chromatin accessibility profiles of individual cells. The simulated doublets are then embedded alongside the original cells using the spectral embedding algorithm in this package. A k-nearest-neighbor classifier is trained to distinguish between the simulated doublets and the authentic cells. This trained classifier produces a “doublet score” for each cell. The doublet scores are then converted into probabilities using a Gaussian mixture model.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	774
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	775 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	776 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.scrublet.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	777
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	778 Remove doublets according to the doublet probability or doublet score, using `pp.filter_doublets`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	779 =================================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	780
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	781 Remove doublets according to the doublet probability or doublet score.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	782
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	783 The user can choose to remove doublets by either the doublet probability or the doublet score. `scrublet` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	784
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	785 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	786 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.filter_doublets.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	787
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	788 A modified MNN-Correct algorithm based on cluster centroid, using `pp.mnc_correct`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	789 ==================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	790
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	791 A modified MNN-Correct algorithm based on cluster centroid.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	792
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	793 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	794 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.mnc_correct.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	795
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	796 Use harmonypy to integrate different experiments,using `pp.harmony`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	797 ===================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	798
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	799 Use harmonypy to integrate different experiments.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	800
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	801 Harmony is an algorithm for integrating single-cell data from multiple experiments. This function uses the python port of Harmony, `harmonypy`, to integrate single-cell data stored in an AnnData object. This function should be run after performing dimension reduction.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	802
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	803 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	804 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.harmony.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	805
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	806 Use Scanorama to integrate different experiments, using `pp.scanorama_integrate`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	807 ========================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	808
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	809 Use Scanorama to integrate different experiments.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	810
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	811 Scanorama is an algorithm for integrating single-cell data from multiple experiments stored in an AnnData object. This function should be run after performing `tl.spectral` but before computing the neighbor graph.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	812
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	813 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	814 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.scanorama_integrate.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	815
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	816 Compute the fragment size distribution of the dataset, using `metrics.frag_size_distr`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	817 ======================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	818
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	819 Compute the fragment size distribution of the dataset.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	820
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	821 This function computes the fragment size distribution of the dataset. Note that it does not operate at the single-cell level. The result is stored in a vector where each element represents the number of fragments and the index represents the fragment length. The first posision of the vector is reserved for fragments with size larger than the `max_recorded_size` parameter. `import_data` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	822
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	823 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	824 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.metrics.frag_size_distr.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	825
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	826 Compute the TSS enrichment score (TSSe) for each cell, using `metrics.tsse`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	827 ===========================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	828
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	829 Compute the TSS enrichment score (TSSe) for each cell.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	830
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	831 `import_data` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	832
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	833 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	834 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.metrics.tsse.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	835
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	836 ]]></help>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	837 <expand macro="citations"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b iuc parents: diff changeset	838 </tool>

Mercurial > repos > iuc > snapatac2_preprocessing

annotate preprocessing.xml @ 3:3d1103801ff2 draft