Mercurial > repos > iuc > snapatac2_preprocessing

annotate preprocessing.xml @ 6:20c4011e1458 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
author iuc
date Tue, 25 Nov 2025 16:40:47 +0000
parents c5c94e01a1b5
children
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1 <tool id="snapatac2_preprocessing" name="SnapATAC2 Preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>and integration</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <requirements>
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8 <expand macro="requirements"/>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #if $method.method != 'pp.make_fragment_file' and $method.method != 'pp.import_contacts' and $method.method != 'pp.import_fragments'
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12 @CMD_PREP_ADATA@
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13 #end if
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14 @CMD@
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15 ]]></command>
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16 <configfiles>
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17 <configfile name="script_file"><![CDATA[
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18 @CONF_IMPORTS@
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19
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20 #if $method.method != 'pp.make_fragment_file' and $method.method != 'pp.import_contacts' and $method.method != 'pp.import_fragments'
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21 @CONF_READ_INPUTS@
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22 #end if
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24 #if $method.method == 'pp.make_fragment_file'
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25 snap.pp.make_fragment_file(
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26 bam_file = '$method.bam_file',
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27 is_paired = $method.is_paired,
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28 #if $method.barcode.extract_type == 'from_tag'
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29 #if $method.barcode.barcode_tag != ''
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30 barcode_tag = '$method.barcode.barcode_tag',
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31 #end if
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32 #else if $method.barcode.extract_type == 'from_read_names'
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33 #if $method.barcode.barcode_regex != ''
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34 barcode_regex = '$method.barcode.barcode_regex',
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35 #end if
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36 #end if
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37 #if $method.umi_tag != ''
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38 umi_tag = '$method.umi_tag',
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39 #end if
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40 #if $method.umi_regex != ''
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41 umi_regex = '$method.umi_regex',
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42 #end if
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43 shift_right = $method.shift_right,
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44 shift_left = $method.shift_left,
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45 min_mapq = $method.min_mapq,
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46 chunk_size = $method.chunk_size,
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47 compression = 'gzip',
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48 output_file = '$fragments_out',
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49 tempdir = "."
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50 )
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51
6
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52 #else if $method.method == 'pp.import_fragments'
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53
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54 chrom_sizes = {}
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55 with open('$method.chrom_sizes', 'r') as f:
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56 for line in f:
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57 chrom, size = line.strip().split('\t')
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58 chrom_sizes[chrom] = int(size)
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59
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60 ## suggested by authors: https://github.com/scverse/SnapATAC2/blob/5a87c5ad4e0c4008fa9b58907a85b542073287b4/snapatac2-python/python/snapatac2/preprocessing/_basic.py#L244
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61 if __name__ == '__main__':
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62 adata = snap.pp.import_fragments(
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63 fragment_file = '$method.fragment_file',
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64 chrom_sizes = chrom_sizes,
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65 min_num_fragments = $method.min_num_fragments,
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66 sorted_by_barcode = $method.sorted_by_barcode,
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67 #if $method.whitelist:
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68 whitelist = '$method.whitelist',
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69 #end if
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70 #if $method.chrM != ''
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71 #set $chrM = ([x.strip() for x in str($method.chrM).split(',')])
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72 chrM = $chrM,
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73 #end if
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74 shift_left = $method.shift_left,
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75 shift_right = $method.shift_right,
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76 chunk_size = $method.chunk_size,
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77 tempdir = ".",
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78 backend = 'hdf5',
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79 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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80 )
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81 ## Not sure how this should work and there is no documentation for it.
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82 ## #else if $method.method == 'pp.import_values'
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83 ## chrom_sizes = {}
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84 ## with open('$method.chrom_sizes', 'r') as f:
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85 ## for line in f:
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86 ## chrom, size = line.strip().split('\t')
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87 ## chrom_sizes[chrom] = int(size)
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88 ##
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89 ## snap.pp.import_values(
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90 ## input_dir = 'input',
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91 ## file = '$anndata_out',
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92 ## chrom_sizes = chrom_sizes,
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93 ## chunk_size = $method.chunk_size,
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94 ## backend = 'hdf5'
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95 ## )
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96
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97 #else if $method.method == 'pp.import_contacts'
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98 chrom_sizes = {}
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99 with open('$method.chrom_sizes', 'r') as f:
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100 for line in f:
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101 chrom, size = line.strip().split('\t')
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102 chrom_sizes[chrom] = int(size)
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103
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104 adata = snap.pp.import_contacts(
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105 contact_file = '$method.contact_file',
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106 chrom_sizes = chrom_sizes,
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107 sorted_by_barcode = $method.sorted_by_barcode,
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108 bin_size = $method.bin_size,
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109 chunk_size = $method.chunk_size,
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110 tempdir = ".",
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111 backend = 'hdf5'
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112 )
6
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113 ## Not sure how this should work and there is no documentation for it.
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114 ## #else if $method.method == 'pp.call_cells'
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115 ## snap.pp.call_cells(
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116 ## adata,
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117 ## use_rep = $method.use_rep,
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118 ## inplace = True,
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119 ## n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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120 ## )
0
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121
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122 #else if $method.method == 'pp.add_tile_matrix'
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123 snap.pp.add_tile_matrix(
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124 adata,
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125 bin_size = $method.bin_size,
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126 inplace = True,
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127 chunk_size = $method.chunk_size,
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128 #if $method.exclude_chroms != ''
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129 #set $excl_chroms = ([x.strip() for x in str($method.exclude_chroms).split(',')])
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130 exclude_chroms = $excl_chroms,
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131 #end if
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132 #if $method.min_frag_size
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133 min_frag_size = $method.min_frag_size,
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134 #end if
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135 #if $method.max_frag_size
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136 max_frag_size = $method.max_frag_size,
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137 #end if
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138 counting_strategy = '$method.counting_strategy',
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139 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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140 )
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141
6
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142
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143
0
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144 #else if $method.method == 'pp.make_gene_matrix'
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145 adata = snap.pp.make_gene_matrix(
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146 adata,
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147 #if $method.gff_file_condi.gffSource == 'cached':
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148 gene_anno = '$method.gff_file_condi.gff_pre_installed.fields.path',
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149 #else:
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150 gene_anno = '$method.gff_file_condi.gff_history',
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151 #end if
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152 inplace = False,
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153 chunk_size = $method.chunk_size,
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154 use_x = $method.use_x,
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155 id_type = '$method.id_type',
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156 upstream = $method.upstream,
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157 downstream = $method.downstream,
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158 include_gene_body = $method.include_gene_body,
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159 transcript_name_key = '$method.transcript_name_key',
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160 transcript_id_key = '$method.transcript_id_key',
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161 gene_name_key = '$method.gene_name_key',
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162 gene_id_key = '$method.gene_id_key',
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163 #if $method.min_frag_size
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164 min_frag_size = $method.min_frag_size,
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165 #end if
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166 #if $method.max_frag_size
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167 max_frag_size = $method.max_frag_size,
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168 #end if
3
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169 counting_strategy = '$method.counting_strategy'
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170 )
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171
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172 #else if $method.method == 'pp.filter_cells'
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173 snap.pp.filter_cells(
1
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174 adata,
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175 min_counts = $method.min_counts,
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176 min_tsse = $method.min_tsse,
6
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177 #if str($method.max_counts) != '':
1
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178 max_counts = $method.max_counts,
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179 #end if
6
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180 #if str($method.max_tsse) != '':
1
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181 max_tsse = $method.max_tsse,
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182 #end if
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183 inplace = True,
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184 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
0
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185 )
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186
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187 #else if $method.method == 'pp.select_features'
6
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188 snap.pp.select_features(
1
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189 adata,
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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190 n_features = $method.n_features,
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191 filter_lower_quantile = $method.filter_lower_quantile,
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192 filter_upper_quantile = $method.filter_upper_quantile,
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193 #if str($method.whitelist) != 'None'
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194 whitelist = '$method.whitelist',
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195 #end if
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196 #if str($method.blacklist) != 'None'
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197 blacklist = '$method.blacklist',
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198 #end if
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199 max_iter = $method.max_iter,
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200 inplace = True,
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201 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
0
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202 )
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203
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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204 #else if $method.method == 'pp.scrublet'
6
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205 ## somewhere in the SnapATAC2 code, a pandas Series is being passed where a numpy array is expected.
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206 ## This is a workaround to add the nonzero method back to pandas Series.
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207 ## Add the nonzero method back to pandas Series
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208 import pandas as pd
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209 def series_nonzero(self):
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210 return (self != 0).values.nonzero()
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211
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212 pd.Series.nonzero = series_nonzero
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213
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214 snap.pp.scrublet(
1
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215 adata,
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216 #if $method.features
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217 features = '$method.features',
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218 #end if
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219 n_comps = $method.n_comps,
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220 sim_doublet_ratio = $method.sim_doublet_ratio,
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221 expected_doublet_rate = $method.expected_doublet_rate,
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222 #if $method.n_neighbors
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223 n_neighbors = $method.n_neighbors,
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224 #end if
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225 use_approx_neighbors = $method.use_approx_neighbors,
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226 random_state = $method.random_state,
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227 inplace = True,
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228 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
0
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229 )
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230
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231 #else if $method.method == 'pp.filter_doublets'
6
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232 snap.pp.filter_doublets(
1
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233 adata,
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234 #if $method.probability_threshold
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235 probability_threshold = $method.probability_threshold,
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236 #end if
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237 #if $method.score_threshold
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238 score_threshold = $method.score_threshold,
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239 #end if
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240 inplace = True,
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241 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
0
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242 )
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243
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244 #else if $method.method == 'pp.mnc_correct'
6
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245 snap.pp.mnc_correct(
1
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246 adata,
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247 batch = '$method.batch',
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248 n_neighbors = $method.n_neighbors,
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249 n_clusters = $method.n_clusters,
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250 n_iter = $method.n_iter,
6
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251 @CONF_PARAMS_DATA_INTEGRATION@
1
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252 inplace = True,
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253 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
0
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254 )
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255
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256 #else if $method.method == 'pp.harmony'
6
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257 snap.pp.harmony(
1
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258 adata,
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259 batch = '$method.batch',
6
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260 @CONF_PARAMS_DATA_INTEGRATION@
1
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261 inplace = True
0
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262 )
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263
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264 #else if $method.method == 'pp.scanorama_integrate'
6
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265 snap.pp.scanorama_integrate(
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266 adata,
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267 batch = '$method.batch',
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268 n_neighbors = $method.n_neighbors,
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269 @CONF_PARAMS_DATA_INTEGRATION@
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270 inplace = True
0
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271 )
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272
6
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273 #else if $method.method == 'ex.export_fragments'
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274 snap.ex.export_fragments(
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275 adata,
6
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276 groupby = '$method.groupby',
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277 #if $method.min_frag_length:
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278 min_frag_length = $method.min_frag_length,
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279 #end if
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280 #if $method.max_frag_length:
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281 max_frag_length = $method.max_frag_length,
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282 #end if
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283 out_dir='./fragments',
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284 suffix = '.bed.gz',
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285 compression = 'gzip'
0
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286 )
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287
6
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288 #else if $method.method == 'ex.export_coverage'
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289 snap.ex.export_coverage(
1
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290 adata,
6
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291 groupby = '$method.groupby',
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292 selections = None, # will add if requested by users
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293 bin_size = $method.bin_size,
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294 #if $method.blacklist:
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295 blacklist = $method.blacklist,
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296 #end if
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297 normalization = '$method.normalization',
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298 #if $method.include_for_norm:
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299 include_for_norm = '$method.include_for_norm',
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300 #end if
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301 #if $method.exclude_for_norm:
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302 exclude_for_norm = '$method.exclude_for_norm',
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303 #end if
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304 #if $method.min_frag_length:
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305 min_frag_length = $method.min_frag_length,
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306 #end if
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307 max_frag_length = $method.max_frag_length,
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308 counting_strategy = '$method.counting_strategy',
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309 #if $method.smooth_base:
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310 smooth_base = $method.smooth_base,
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311 #end if
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312 out_dir = './coverage',
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313 #if str($method.output_format) == 'bedgraph':
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314 suffix = '.bedgraph.gz',
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315 #else
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316 suffix = '.bigwig',
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317 #end if
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318 output_format = '$method.output_format',
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319 #if $method.output_format == 'bedgraph':
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320 compression = 'gzip',
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321 #end if
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322 tempdir = '.',
1
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323 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
0
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324 )
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325 #end if
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326
6
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327 #if $method.method != 'pp.make_fragment_file' and $method.method != 'ex.export_fragments' and $method.method != 'ex.export_coverage'
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328 @CONF_ANNDATA_WRITE_OUTPUTS@
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329 #end if
1
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330 ]]></configfile>
0
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331 </configfiles>
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332 <inputs>
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333 <conditional name="method">
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334 <param name="method" type="select" label="Method used for preprocessing">
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335 <option value="pp.make_fragment_file">Convert a BAM file to a fragment file, using 'pp.make_fragment_file'</option>
6
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336 <option value="pp.import_fragments">Import data fragment files and compute basic QC metrics, using 'pp.import_fragments'</option>
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337 <!-- Not sure how this should work and there is no documentation for it. -->
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338 <!-- <option value="pp.import_values">Import values associated with base pairs, using 'pp.import_values'</option> -->
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339 <option value="pp.import_contacts">Import chromatin contacts, using 'pp.import_contacts'</option>
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340 <!-- Not sure how this should work and there is no documentation for it. -->
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341 <!-- <option value="pp.call_cells">Calling cells based on the number of feature counts, using 'pp.call_cells'</option> -->
0
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342 <option value="pp.add_tile_matrix">Generate cell by bin count matrix, using 'pp.add_tile_matrix'</option>
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343 <option value="pp.make_gene_matrix">Generate cell by gene activity matrix, using 'pp.make_gene_matrix'</option>
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344 <option value="pp.filter_cells">Filter cell outliers based on counts and numbers of genes expressed, using 'pp.filter_cells'</option>
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345 <option value="pp.select_features">Perform feature selection, using 'pp.select_features'</option>
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346 <option value="pp.scrublet">Compute probability of being a doublet using the scrublet algorithm, using 'pp.scrublet'</option>
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347 <option value="pp.filter_doublets">Remove doublets according to the doublet probability or doublet score, using 'pp.filter_doublets'</option>
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348 <option value="pp.mnc_correct">A modified MNN-Correct algorithm based on cluster centroid, using 'pp.mnc_correct'</option>
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349 <option value="pp.harmony">Use harmonypy to integrate different experiments,using 'pp.harmony'</option>
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350 <option value="pp.scanorama_integrate">Use Scanorama [Hie19] to integrate different experiments, using 'pp.scanorama_integrate'</option>
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351 <option value="ex.export_fragments">Export and save fragments in a BED format file, using 'ex.export_fragments'</option>
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352 <option value="ex.export_coverage">Export and save coverage information in a bedgraph or bigwig format file, using 'ex.export_coverage'</option>
0
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353 </param>
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354 <when value="pp.make_fragment_file">
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355 <param argument="bam_file" type="data" format="bam" label="File name of the BAM file"/>
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356 <param argument="is_paired" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Indicate whether the BAM file contain paired-end reads"/>
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357 <conditional name="barcode">
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358 <param name="extract_type" type="select" label="How to extract barcodes from BAM records?">
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359 <option value="from_tag">From TAG fields</option>
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360 <option value="from_read_names">From read names using regular expressions</option>
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361 </param>
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362 <when value="from_tag">
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363 <param argument="barcode_tag" type="text" value="CB" optional="true" label="Extract barcodes from TAG fields of BAM records"/>
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364 </when>
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365 <when value="from_read_names">
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366 <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``"/>
0
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367 </when>
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368 </conditional>
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369 <param argument="umi_tag" type="text" value="" optional="true" label="Extract UMI from TAG fields of BAM records"/>
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370 <param argument="umi_regex" type="text" value="" optional="true" label="Extract UMI from read names of BAM records using regular expressions"/>
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371 <expand macro="param_shift" varname="shift_left" label="Shift left" value="4"/>
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372 <expand macro="param_shift" varname="shift_right" label="Shift right" value="-5"/>
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373 <param argument="min_mapq" type="integer" min="0" value="30" label="Filter the reads based on MAPQ"/>
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374 <expand macro="param_chunk_size" size="50000000"/>
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375 </when>
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376 <when value="pp.import_fragments">
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377 <param argument="fragment_file" type="data" format="bed" label="Fragment file to import" help=" A fragment file must contain at least 5 columns: chromosome, start, end, barcode, count"/>
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378 <expand macro="param_chrom_sizes"/>
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379 <param argument="min_num_fragments" type="integer" value="200" label="Minimum number of fragments required for a cell to pass filtering"/>
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380 <param argument="sorted_by_barcode" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether the fragment file is sorted by barcode"/>
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381 <param argument="whitelist" type="data" format="bed" optional="true" label="A user provided bed file containing genome-wide whitelist regions"/>
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382 <param argument="chrM" type="text" value="" optional="true" label="A list of chromosomes to be treated as mitochondrial chromosomes, e.g. chrM, M, mt, mtDNA">
0
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383 <expand macro="sanitize_query"/>
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384 </param>
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385 <expand macro="param_shift" varname="shift_left" label="Shift left" value="0"/>
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386 <expand macro="param_shift" varname="shift_right" label="Shift right" value="0"/>
0
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387 <expand macro="param_chunk_size" size="2000"/>
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388 </when>
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389 <!-- Not sure how this should work and there is no documentation for it. -->
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390 <!-- <when value="pp.import_values">
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391 <expand macro="param_inputs_anndata" multiple="true"/>
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392 <expand macro="param_chrom_sizes"/>
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393 <expand macro="param_chunk_size" size="200"/>
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394 </when> -->
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395 <when value="pp.import_contacts">
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396 <param argument="contact_file" type="data" format="bed" label="Contact file to import"/>
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397 <expand macro="param_chrom_sizes"/>
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398 <param argument="sorted_by_barcode" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether the contact file is sorted by barcode"/>
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399 <param argument="bin_size" type="integer" value="500000" label="The size of consecutive genomic regions used to record the counts"/>
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400 <expand macro="param_chunk_size" size="200"/>
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401 </when>
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402 <!-- Not sure how this should work and there is no documentation for it. -->
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403 <!-- <when value="pp.call_cells">
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404 <expand macro="param_inputs_anndata"/>
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405 <param argument="use_rep" type="float" value="" optional="true" label="The representation to use for filtering"/>
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406 </when> -->
0
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407 <when value="pp.add_tile_matrix">
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408 <expand macro="param_inputs_anndata"/>
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409 <param argument="bin_size" type="integer" value="500" label="The size of consecutive genomic regions used to record the counts"/>
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410 <expand macro="param_chunk_size" size="500"/>
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411 <param argument="exclude_chroms" type="text" value="chrM, chrY, M, Y" optional="true" label="A list of chromosomes to exclude">
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412 <expand macro="sanitize_query"/>
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413 </param>
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414 <expand macro="param_min_max_frag_size"/>
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415 <expand macro="param_counting_strategy"/>
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416 </when>
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417 <when value="pp.make_gene_matrix">
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418 <expand macro="param_inputs_anndata"/>
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419 <expand macro="param_gene_anno"/>
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420 <expand macro="param_chunk_size" size="500"/>
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421 <param argument="use_x" type="boolean" truevalue="True" falsevalue="False" checked="false" label="If True, use the matrix stored in .X as raw counts"/>
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422 <param argument="id_type" type="select" label="Id type, 'gene' or 'transcript'">
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423 <option value="gene" selected="true">gene</option>
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424 <option value="transcript">transcript</option>
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425 </param>
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426 <param argument="upstream" type="integer" value="2000" label="Number of base pairs upstream of the regulatory domain"/>
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427 <param argument="downstream" type="integer" value="0" label="Number of base pairs downstream of regulatory domain"/>
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428 <param argument="include_gene_body" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to include the gene body in the regulatory domain. If False, the TSS is used as the regulatory domain."/>
0
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429 <param argument="transcript_name_key" type="text" value="transcript_name" label="The key of the transcript name in the gene annotation file"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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diff changeset
430 <param argument="transcript_id_key" type="text" value="transcript_id" label="The key of the transcript id in the gene annotation file"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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431 <param argument="gene_name_key" type="text" value="gene_name" label="The key of the gene name in the gene annotation file"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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432 <param argument="gene_id_key" type="text" value="gene_id" label="The key of the gene id in the gene annotation file"/>
6
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433 <expand macro="param_min_max_frag_size"/>
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parents: 2
diff changeset
434 <expand macro="param_counting_strategy"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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435 </when>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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diff changeset
436 <when value="pp.filter_cells">
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iuc
parents: 5
diff changeset
437 <expand macro="param_inputs_anndata"/>
0
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438 <param argument="min_counts" type="integer" value="1000" label="Minimum number of counts required for a cell to pass filtering"/>
6
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parents: 5
diff changeset
439 <param argument="min_tsse" type="float" value="5.0" label="Minimum TSS enrichment score required for a cell to pass filtering"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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440 <param argument="max_counts" type="integer" value="" optional="true" label="Maximum number of counts required for a cell to pass filtering"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
441 <param argument="max_tsse" type="float" value="" optional="true" label="Maximum TSS enrichment score expressed required for a cell to pass filtering"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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442 </when>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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443 <when value="pp.select_features">
6
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parents: 5
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444 <expand macro="param_inputs_anndata"/>
0
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445 <param argument="n_features" type="integer" min="1" value="500000" label="Number of features to keep"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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446 <param argument="filter_lower_quantile" type="float" min="0" value="0.005" label="Lower quantile of the feature count distribution to filter out"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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447 <param argument="filter_upper_quantile" type="float" min="0" value="0.005" label="Upper quantile of the feature count distribution to filter out"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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448 <param argument="whitelist" type="data" format="bed" optional="true" label="A user provided bed file containing genome-wide whitelist regions"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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449 <param argument="blacklist" type="data" format="bed" optional="true" label="A user provided bed file containing genome-wide blacklist regions"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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450 <param argument="max_iter" type="integer" value="1" label="If greater than 1, this function will perform iterative clustering and feature selection"/>
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451 </when>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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452 <when value="pp.scrublet">
6
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parents: 5
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453 <expand macro="param_inputs_anndata"/>
0
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454 <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."/>
6
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455 <expand macro="param_n_comps" value="15" label="Number of components" help="15 is usually sufficient. The algorithm is not sensitive to this parameter"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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456 <param argument="sim_doublet_ratio" type="float" value="2.0" label="Number of doublets to simulate relative to the number of observed cells"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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457 <param argument="expected_doublet_rate" type="float" value="0.1" label="Expected doublet rate"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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458 <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"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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459 <param argument="use_approx_neighbors" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Whether to use approximate search"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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460 <param argument="random_state" type="integer" value="0" label="Random state"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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461 </when>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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diff changeset
462 <when value="pp.filter_doublets">
6
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iuc
parents: 5
diff changeset
463 <expand macro="param_inputs_anndata"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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464 <param argument="probability_threshold" type="float" value="0.5" label="Threshold for doublet probability"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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diff changeset
465 <param argument="score_threshold" type="float" value="" optional="true" label="Threshold for doublet score"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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466 </when>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
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467 <when value="pp.mnc_correct">
6
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parents: 5
diff changeset
468 <expand macro="param_inputs_anndata"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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469 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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470 <expand macro="sanitize_query"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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diff changeset
471 </param>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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diff changeset
472 <param argument="n_neighbors" type="integer" value="5" label="Number of mutual nearest neighbors"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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diff changeset
473 <param argument="n_clusters" type="integer" value="40" label="Number of clusters"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
474 <param argument="n_iter" type="integer" value="1" label="Number of iterations"/>
6
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parents: 5
diff changeset
475 <expand macro="param_data_integration"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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diff changeset
476 </when>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
477 <when value="pp.harmony">
6
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iuc
parents: 5
diff changeset
478 <expand macro="param_inputs_anndata"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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diff changeset
479 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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diff changeset
480 <expand macro="sanitize_query"/>
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diff changeset
481 </param>
6
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iuc
parents: 5
diff changeset
482 <expand macro="param_data_integration"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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483 </when>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
484 <when value="pp.scanorama_integrate">
6
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parents: 5
diff changeset
485 <expand macro="param_inputs_anndata"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
486 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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diff changeset
487 <expand macro="sanitize_query"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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diff changeset
488 </param>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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489 <param argument="n_neighbors" type="integer" value="20" label="Number of mutual nearest neighbors"/>
6
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parents: 5
diff changeset
490 <expand macro="param_data_integration"/>
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diff changeset
491 </when>
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iuc
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diff changeset
492 <when value="ex.export_fragments">
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iuc
parents: 5
diff changeset
493 <expand macro="param_inputs_anndata"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
494 <expand macro="param_groupby"/>
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parents: 5
diff changeset
495 <param argument="--min_frag_length" type="integer" optional="true" min="0" value="" label="Minimum fragment length to be included in the computation"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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diff changeset
496 <param argument="--max_frag_length" type="integer" optional="true" min="0" value="" label="Maximum fragment length to be included in the computation"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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497 </when>
6
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iuc
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diff changeset
498 <when value="ex.export_coverage">
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iuc
parents: 5
diff changeset
499 <expand macro="param_inputs_anndata"/>
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iuc
parents: 5
diff changeset
500 <expand macro="param_groupby"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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diff changeset
501 <param argument="--bin_size" type="integer" min="0" value="10" label="Size of the bins, in bases, for the output of the bigwig/bedgraph file"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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diff changeset
502 <param argument="--blacklist" type="data" format="bed" optional="true" label="A BED file containing the blacklisted regions"/>
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diff changeset
503 <param argument="--normalization" type="select" label="Normalization method for coverage calculation">
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diff changeset
504 <option value="RPKM" selected="true">RPKM (per bin) = #reads per bin / (#mapped_reads (in millions) * bin length (kb))</option>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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diff changeset
505 <option value="None">No normalization</option>
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iuc
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diff changeset
506 <option value="CPM">CPM (per bin) = #reads per bin / #mapped_reads (in millions)</option>
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iuc
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diff changeset
507 <option value="BPM">BPM (per bin) = #reads per bin / sum of all reads per bin (in millions)</option>
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diff changeset
508 </param>
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iuc
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diff changeset
509 <param argument="--include_for_norm" type="data" format="bed" optional="true" label="A BED file containing the genomic loci to include for normalization"/>
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diff changeset
510 <param argument="--exclude_for_norm" type="data" format="bed" optional="true" label="A BED file containing the genomic loci to exclude for normalization"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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diff changeset
511 <param argument="--min_frag_length" type="integer" optional="true" min="0" value="" label="Minimum fragment length to be included in the computation"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
512 <param argument="--max_frag_length" type="integer" min="0" value="2000" label="Maximum fragment length to be included in the computation"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
513 <param argument="--counting_strategy" type="select" label="The strategy to compute feature counts">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
514 <option value="fragment" selected="true">fragment- the feature counts are assigned based on the number of fragments that overlap with a region of interest</option>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
515 <option value="insertion">insertion - the feature counts are assigned based on the number of insertions that overlap with a region of interest</option>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
516 <option value="paired-insertion">paired-insertion - same as insertion but it only counts the insertions once if the pair of insertions of a fragment are both within the same region of interest</option>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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diff changeset
517 </param>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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diff changeset
518 <param argument="--smooth_base" type="integer" optional="true" min="0" value="" label="Length of the smoothing window in bases for the output of the bigwig/bedgraph file"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
519 <param argument="--output_format" type="select" label="The output format">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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diff changeset
520 <option value="bigwig" selected="true">bigwig</option>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
521 <option value="bedgraph">bedgraph</option>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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diff changeset
522 </param>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
523 </when>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
524 </conditional>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
525 <expand macro="param_common_advanced"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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diff changeset
526 </inputs>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
527 <outputs>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
528 <data name="fragments_out" format="interval" label="${tool.name} (${method.method}) on ${on_string}: Fragment file">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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diff changeset
529 <filter>method['method'] == 'pp.make_fragment_file'</filter>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
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diff changeset
530 </data>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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diff changeset
531 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad.gz" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
532 <filter>method['method'] != 'pp.make_fragment_file' and method['method'] != 'ex.export_fragments' and method['method'] != 'ex.export_coverage'</filter>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
533 <change_format>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
534 <when input="method.method" value="pp.import_fragments" format="h5" />
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
535 </change_format>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
536 </data>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
537 <collection name="export_fragment" type="list" format="bed" label="${tool.name} (${method.method}) on ${on_string}: exported fragments">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
538 <discover_datasets pattern="__name_and_ext__" directory="fragments"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
539 <filter>method['method'] == 'ex.export_fragments'</filter>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
540 </collection>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
541 <collection name="export_coverage" type="list" label="${tool.name} (${method.method}) on ${on_string}: exported coverage">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
542 <discover_datasets pattern="__name_and_ext__" directory="coverage"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
543 <filter>method['method'] == 'ex.export_coverage'</filter>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
544 </collection>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
545 <data name="hidden_output" format="txt" label="Log file">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
546 <filter>advanced_common['show_log']</filter>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
547 </data>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
548 </outputs>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
549 <tests>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
550 <test expect_num_outputs="1">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
551 <!-- pp.make_fragment_file -->
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
552 <conditional name="method">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
553 <param name="method" value="pp.make_fragment_file"/>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
554 <param name="bam_file" location="https://zenodo.org/records/17512085/files/pbmc_500_chr21_subsample.bam"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
555 <param name="is_paired" value="true"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
556 <conditional name="barcode">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
557 <param name="extract_type" value="from_tag"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
558 <param name="barcode_tag" value="CB"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
559 </conditional>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
560 <param name="shift_left" value="4"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
561 <param name="shift_right" value="-5"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
562 <param name="min_mapq" value="10"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
563 <param name="chunk_size" value="50000000"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
564 </conditional>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
565 <output name="fragments_out" location="https://zenodo.org/records/17512085/files/pp.make_fragment_file.pbmc_500_chr21.tsv.gz" ftype="interval" compare="sim_size" delta_frac="0.1"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
566 </test>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
567 <test expect_num_outputs="2">
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
568 <!-- pp.import_fragments -->
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
569 <conditional name="method">
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
570 <param name="method" value="pp.import_fragments"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
571 <param name="fragment_file" location="https://zenodo.org/records/17512085/files/pp.make_fragment_file.pbmc_500_chr21.tsv.gz"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
572 <param name="chrom_sizes" location="https://zenodo.org/records/17512085/files/chrom_size.tabular"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
573 <param name="min_num_fragments" value="200"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
574 <param name="sorted_by_barcode" value="true"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
575 <param name="chrM" value="" />
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
576 <param name="shift_left" value="0"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
577 <param name="shift_right" value="0"/>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
578 <param name="chunk_size" value="2000"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
579 </conditional>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
580 <section name="advanced_common">
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
581 <param name="show_log" value="true" />
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
582 </section>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
583 <output name="hidden_output">
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
584 <assert_contents>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
585 <has_text_matching expression="snap.pp.import_fragments"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
586 <has_text_matching expression="chrom_sizes"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
587 <has_text_matching expression="shift_left = 0"/>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
588 <has_text_matching expression="shift_right = 0"/>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
589 <has_text_matching expression="chunk_size = 2000"/>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
590 </assert_contents>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
591 </output>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
592 <output name="anndata_out" ftype="h5">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
593 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
594 <has_h5_keys keys="obs/n_fragment,obs/frac_dup,obs/frac_mito"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
595 <has_h5_keys keys="uns/reference_sequences"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
596 <has_h5_keys keys="obsm/fragment_paired"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
597 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
598 </output>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
599 </test>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
600 <test expect_num_outputs="2">
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
601 <!-- pp.make_gene_matrix - history -->
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
602 <conditional name="method">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
603 <param name="method" value="pp.make_gene_matrix"/>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
604 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
605 <conditional name="gff_file_condi">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
606 <param name="gffSource" value="history"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
607 <param name="gff_history" location="https://zenodo.org/records/17512085/files/chr21.gff3.gz"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
608 </conditional>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
609 <param name="chunk_size" value="500"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
610 <param name="use_x" value="False"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
611 <param name="id_type" value="gene"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
612 <param name="transcript_name_key" value="transcript_name"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
613 <param name="transcript_id_key" value="transcript_id"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
614 <param name="gene_name_key" value="gene_name"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
615 <param name="gene_id_key" value="gene_id"/>
3
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
616 <param name="counting_strategy" value="insertion"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
617 </conditional>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
618 <section name="advanced_common">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
619 <param name="show_log" value="true" />
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
620 </section>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
621 <output name="hidden_output">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
622 <assert_contents>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
623 <has_text_matching expression="snap.pp.make_gene_matrix"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
624 <has_text_matching expression="chunk_size = 500"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
625 <has_text_matching expression="use_x = False"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
626 <has_text_matching expression="id_type = 'gene'"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
627 <has_text_matching expression="transcript_name_key = 'transcript_name'"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
628 <has_text_matching expression="transcript_id_key = 'transcript_id'"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
629 <has_text_matching expression="gene_name_key = 'gene_name'"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
630 <has_text_matching expression="gene_id_key = 'gene_id'"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
631 <has_text_matching expression="counting_strategy = 'insertion'"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
632 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
633 </output>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
634 <output name="anndata_out" ftype="h5ad">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
635 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
636 <has_h5_keys keys="obs/n_fragment,obs/frac_dup,obs/tsse"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
637 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
638 </output>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
639 </test>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
640 <test expect_num_outputs="2">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
641 <!-- pp.make_gene_matrix - cached -->
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
642 <conditional name="method">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
643 <param name="method" value="pp.make_gene_matrix"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
644 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
645 <conditional name="gff_file_condi">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
646 <param name="gffSource" value="cached"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
647 <param name="gff_pre_installed" value="hg38"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
648 </conditional>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
649 <param name="chunk_size" value="500"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
650 <param name="use_x" value="False"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
651 <param name="id_type" value="gene"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
652 <param name="transcript_name_key" value="transcript_name"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
653 <param name="transcript_id_key" value="transcript_id"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
654 <param name="gene_name_key" value="gene_name"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
655 <param name="gene_id_key" value="gene_id"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
656 <param name="counting_strategy" value="insertion"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
657 </conditional>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
658 <section name="advanced_common">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
659 <param name="show_log" value="true" />
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
660 </section>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
661 <output name="hidden_output">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
662 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
663 <has_text_matching expression="snap.pp.make_gene_matrix"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
664 <has_text_matching expression="chunk_size = 500"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
665 <has_text_matching expression="use_x = False"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
666 <has_text_matching expression="id_type = 'gene'"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
667 <has_text_matching expression="transcript_name_key = 'transcript_name'"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
668 <has_text_matching expression="transcript_id_key = 'transcript_id'"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
669 <has_text_matching expression="gene_name_key = 'gene_name'"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
670 <has_text_matching expression="gene_id_key = 'gene_id'"/>
3
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
671 <has_text_matching expression="counting_strategy = 'insertion'"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
672 </assert_contents>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
673 </output>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
674 <output name="anndata_out" ftype="h5ad">
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
675 <assert_contents>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
676 <has_h5_keys keys="obs/n_fragment,obs/frac_dup,obs/tsse"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
677 </assert_contents>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
678 </output>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
679 </test>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
680 <test expect_num_outputs="2">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
681 <!-- pp.filter_cells -->
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
682 <conditional name="method">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
683 <param name="method" value="pp.filter_cells"/>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
684 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
685 <param name="min_counts" value="500"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
686 <param name="min_tsse" value="1"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
687 <param name="max_counts" value="10000"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
688 </conditional>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
689 <section name="advanced_common">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
690 <param name="show_log" value="true" />
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
691 </section>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
692 <assert_stdout>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
693 <has_text_matching expression="6 × 9342"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
694 </assert_stdout>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
695 <output name="hidden_output">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
696 <assert_contents>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
697 <has_text_matching expression="snap.pp.filter_cells"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
698 <has_text_matching expression="min_counts = 500"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
699 <has_text_matching expression="min_tsse = 1"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
700 <has_text_matching expression="max_counts = 10000"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
701 </assert_contents>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
702 </output>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
703 <output name="anndata_out" ftype="h5ad">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
704 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
705 <has_h5_keys keys="obs/n_fragment"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
706 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
707 </output>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
708 </test>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
709 <test expect_num_outputs="2">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
710 <!-- pp.add_tile_matrix -->
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
711 <conditional name="method">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
712 <param name="method" value="pp.add_tile_matrix"/>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
713 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
714 <param name="bin_size" value="5000"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
715 <param name="chunk_size" value="500"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
716 <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"/>
3
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
717 <param name="counting_strategy" value="insertion"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
718 </conditional>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
719 <section name="advanced_common">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
720 <param name="show_log" value="true" />
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
721 </section>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
722 <output name="hidden_output">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
723 <assert_contents>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
724 <has_text_matching expression="snap.pp.add_tile_matrix"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
725 <has_text_matching expression="bin_size = 5000"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
726 <has_text_matching expression="chunk_size = 500"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
727 <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
3
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
728 <has_text_matching expression="counting_strategy = 'insertion'"/>
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
729 </assert_contents>
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
730 </output>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
731 <output name="anndata_out" ftype="h5ad">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
732 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
733 <has_h5_keys keys="obs/n_fragment,obs/frac_dup,obs/frac_mito,obs/tsse"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
734 <has_h5_keys keys="uns/reference_sequences"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
735 <has_h5_keys keys="obsm/fragment_paired"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
736 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
737 </output>
3
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
738 </test>
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
739 <test expect_num_outputs="2">
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
740 <!-- pp.add_tile_matrix counting_strategy fragment -->
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
741 <conditional name="method">
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
742 <param name="method" value="pp.add_tile_matrix"/>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
743 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
3
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
744 <param name="bin_size" value="5000"/>
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
745 <param name="chunk_size" value="500"/>
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
746 <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"/>
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
747 <param name="counting_strategy" value="fragment"/>
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
748 </conditional>
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
749 <section name="advanced_common">
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
750 <param name="show_log" value="true" />
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
751 </section>
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
752 <output name="hidden_output">
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
753 <assert_contents>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
754 <has_text_matching expression="snap.pp.add_tile_matrix"/>
3
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
755 <has_text_matching expression="bin_size = 5000"/>
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
756 <has_text_matching expression="chunk_size = 500"/>
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
757 <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
4ecdea4cbea1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 2
diff changeset
758 <has_text_matching expression="counting_strategy = 'fragment'"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
759 </assert_contents>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
760 </output>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
761 <output name="anndata_out" ftype="h5ad">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
762 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
763 <has_h5_keys keys="obs/n_fragment,obs/frac_dup,obs/tsse"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
764 <has_h5_keys keys="obsm/fragment_paired"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
765 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
766 </output>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
767 </test>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
768 <test expect_num_outputs="2">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
769 <!-- pp.select_features -->
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
770 <conditional name="method">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
771 <param name="method" value="pp.select_features"/>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
772 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
773 <param name="n_features" value="15000"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
774 </conditional>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
775 <section name="advanced_common">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
776 <param name="show_log" value="true" />
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
777 </section>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
778 <output name="hidden_output">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
779 <assert_contents>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
780 <has_text_matching expression="snap.pp.select_features"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
781 <has_text_matching expression="n_features = 15000"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
782 </assert_contents>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
783 </output>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
784 <output name="anndata_out" ftype="h5ad">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
785 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
786 <has_h5_keys keys="var/count,var/selected"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
787 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
788 </output>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
789 </test>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
790 <test expect_num_outputs="2">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
791 <!-- pp.scrublet -->
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
792 <conditional name="method">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
793 <param name="method" value="pp.scrublet"/>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
794 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.select_features.pbmc_500_chr21.h5ad"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
795 <param name="n_comps" value="15"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
796 <param name="sim_doublet_ratio" value="2.0"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
797 <param name="expected_doublet_rate" value="0.1"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
798 <param name="random_state" value="0"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
799 </conditional>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
800 <section name="advanced_common">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
801 <param name="show_log" value="true" />
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
802 </section>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
803 <assert_stdout>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
804 <has_text_matching expression="158 × 9342"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
805 </assert_stdout>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
806 <output name="hidden_output">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
807 <assert_contents>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
808 <has_text_matching expression="snap.pp.scrublet"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
809 <has_text_matching expression="n_comps = 15"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
810 <has_text_matching expression="sim_doublet_ratio = 2.0"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
811 <has_text_matching expression="expected_doublet_rate = 0.1"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
812 <has_text_matching expression="random_state = 0"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
813 </assert_contents>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
814 </output>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
815 <output name="anndata_out" ftype="h5ad">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
816 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
817 <has_h5_keys keys="obs/doublet_probability,obs/doublet_score"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
818 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
819 </output>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
820 </test>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
821 <test expect_num_outputs="2">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
822 <!-- pp.filter_doublets -->
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
823 <conditional name="method">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
824 <param name="method" value="pp.filter_doublets"/>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
825 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.scrublet.pbmc_500_chr21.h5ad"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
826 <param name="probability_threshold" value="0.1"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
827 </conditional>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
828 <section name="advanced_common">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
829 <param name="show_log" value="true" />
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
830 </section>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
831 <assert_stdout>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
832 <has_text_matching expression="156 × 9342"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
833 </assert_stdout>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
834 <output name="hidden_output">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
835 <assert_contents>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
836 <has_text_matching expression="snap.pp.filter_doublets"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
837 </assert_contents>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
838 </output>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
839 <output name="anndata_out" ftype="h5ad">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
840 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
841 <has_h5_keys keys="obs/doublet_probability,obs/doublet_score"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
842 <has_h5_keys keys="uns/doublet_rate"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
843 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
844 </output>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
845 </test>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
846 <test expect_num_outputs="2">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
847 <!-- pp.mnc_correct -->
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
848 <conditional name="method">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
849 <param name="method" value="pp.mnc_correct"/>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
850 <param name="adata" location="https://zenodo.org/records/17512085/files/pbmc_500_chr21.batch.h5ad"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
851 <param name="batch" value="batch"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
852 <param name="n_neighbors" value="3"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
853 <param name="n_clusters" value="10"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
854 <param name="use_rep" value="X_spectral"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
855 </conditional>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
856 <section name="advanced_common">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
857 <param name="show_log" value="true" />
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
858 </section>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
859 <output name="hidden_output">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
860 <assert_contents>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
861 <has_text_matching expression="snap.pp.mnc_correct"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
862 <has_text_matching expression="batch = 'batch'"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
863 <has_text_matching expression="n_neighbors = 3"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
864 <has_text_matching expression="n_clusters = 10"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
865 <has_text_matching expression="batch = 'batch'"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
866 <has_text_matching expression="use_rep = 'X_spectral'"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
867 </assert_contents>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
868 </output>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
869 <output name="anndata_out" ftype="h5ad">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
870 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
871 <has_h5_keys keys="obsm/X_spectral_mnn"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
872 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
873 </output>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
874 </test>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
875 <test expect_num_outputs="2">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
876 <!-- pp.harmony -->
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
877 <conditional name="method">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
878 <param name="method" value="pp.harmony"/>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
879 <param name="adata" location="https://zenodo.org/records/17512085/files/pbmc_500_chr21.batch.h5ad"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
880 <param name="batch" value="batch"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
881 <param name="use_rep" value="X_spectral"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
882 </conditional>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
883 <section name="advanced_common">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
884 <param name="show_log" value="true" />
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
885 </section>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
886 <output name="hidden_output">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
887 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
888 <has_text_matching expression="snap.pp.harmony"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
889 <has_text_matching expression="batch = 'batch'"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
890 <has_text_matching expression="use_rep = 'X_spectral'"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
891 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
892 </output>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
893 <output name="anndata_out" ftype="h5ad">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
894 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
895 <has_h5_keys keys="obsm/X_spectral_harmony"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
896 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
897 </output>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
898 </test>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
899 <test expect_num_outputs="2">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
900 <!-- pp.scanorama_integrate -->
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
901 <conditional name="method">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
902 <param name="method" value="pp.scanorama_integrate"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
903 <param name="adata" location="https://zenodo.org/records/17512085/files/pbmc_500_chr21.batch.h5ad"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
904 <param name="batch" value="batch"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
905 <param name="use_rep" value="X_spectral"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
906 </conditional>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
907 <section name="advanced_common">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
908 <param name="show_log" value="true" />
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
909 </section>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
910 <output name="hidden_output">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
911 <assert_contents>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
912 <has_text_matching expression="snap.pp.scanorama_integrate"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
913 <has_text_matching expression="batch = 'batch'"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
914 <has_text_matching expression="use_rep = 'X_spectral'"/>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
915 </assert_contents>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
916 </output>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
917 <output name="anndata_out" ftype="h5ad">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
918 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
919 <has_h5_keys keys="obsm/X_spectral_scanorama"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
920 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
921 </output>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
922 </test>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
923 <!-- pp.import_contacts -->
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
924 <test expect_num_outputs="2">
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
925 <conditional name="method">
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
926 <param name="method" value="pp.import_contacts"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
927 <param name="contact_file" location="https://zenodo.org/records/17512085/files/pp.make_fragment_file.pbmc_500_chr21.tsv.gz"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
928 <param name="chrom_sizes" location="https://zenodo.org/records/17512085/files/chrom_size.tabular"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
929 </conditional>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
930 <section name="advanced_common">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
931 <param name="show_log" value="true" />
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
932 </section>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
933 <output name="hidden_output">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
934 <assert_contents>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
935 <has_text_matching expression="snap.pp.import_contacts"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
936 <has_text_matching expression="chrom_sizes"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
937 <has_text_matching expression="sorted_by_barcode = True"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
938 <has_text_matching expression="bin_size = 500000"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
939 <has_text_matching expression="chunk_size = 200"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
940 </assert_contents>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
941 </output>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
942 <output name="anndata_out" ftype="h5ad">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
943 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
944 <has_h5_keys keys="uns/reference_sequences"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
945 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
946 </output>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
947 </test>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
948 <test expect_num_outputs="2">
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
949 <!-- ex.export_fragments -->
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
950 <conditional name="method">
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
951 <param name="method" value="ex.export_fragments"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
952 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
953 <param name="groupby" value="leiden"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
954 </conditional>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
955 <section name="advanced_common">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
956 <param name="show_log" value="true" />
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
957 </section>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
958 <output name="hidden_output">
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
959 <assert_contents>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
960 <has_text_matching expression="snap.ex.export_fragments"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
961 <has_text_matching expression="groupby = &apos;leiden&apos;"/>
1
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
962 </assert_contents>
cec3e76eaf05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents: 0
diff changeset
963 </output>
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
964 <output_collection name="export_fragment" type="list" count="8">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
965 <element name="-1.bed">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
966 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
967 <has_n_lines n="1018"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
968 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
969 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
970 <element name="0.bed">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
971 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
972 <has_n_lines n="2973"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
973 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
974 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
975 <element name="1.bed">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
976 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
977 <has_n_lines n="1661"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
978 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
979 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
980 <element name="2.bed">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
981 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
982 <has_n_lines n="1605"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
983 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
984 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
985 <element name="3.bed">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
986 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
987 <has_n_lines n="1457"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
988 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
989 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
990 <element name="4.bed">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
991 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
992 <has_n_lines n="620"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
993 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
994 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
995 <element name="5.bed">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
996 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
997 <has_n_lines n="2618"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
998 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
999 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1000 <element name="6.bed">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1001 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1002 <has_n_lines n="225"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1003 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1004 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1005 </output_collection>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1006 </test>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1007 <test expect_num_outputs="2">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1008 <!-- ex.export_coverage -->
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1009 <conditional name="method">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1010 <param name="method" value="ex.export_coverage"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1011 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1012 <param name="groupby" value="leiden"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1013 </conditional>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1014 <section name="advanced_common">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1015 <param name="show_log" value="true" />
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1016 </section>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1017 <output name="hidden_output">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1018 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1019 <has_text_matching expression="snap.ex.export_coverage"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1020 <has_text_matching expression="groupby = &apos;leiden&apos;"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1021 <has_text_matching expression="output_format = &apos;bigwig&apos;"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1022 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1023 </output>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1024 <output_collection name="export_coverage" type="list" count="8">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1025 <element name="-1">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1026 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1027 <has_n_lines n="981"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1028 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1029 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1030 <element name="0">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1031 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1032 <has_n_lines n="2447"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1033 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1034 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1035 <element name="1">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1036 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1037 <has_n_lines n="1571"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1038 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1039 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1040 <element name="2">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1041 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1042 <has_n_lines n="1499"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1043 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1044 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1045 <element name="3">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1046 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1047 <has_n_lines n="1269"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1048 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1049 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1050 <element name="4">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1051 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1052 <has_n_lines n="640"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1053 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1054 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1055 <element name="5">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1056 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1057 <has_n_lines n="2420"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1058 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1059 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1060 <element name="6">
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1061 <assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1062 <has_n_lines n="177"/>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1063 </assert_contents>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1064 </element>
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1065 </output_collection>
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1066 </test>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1067 </tests>
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1068 <help><![CDATA[
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1069 Convert a BAM file to a fragment file, using `pp.make_fragment_file`
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1070 ====================================================================
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1071
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1072 Convert a BAM file to a fragment file.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1073
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1074 Convert a BAM file to a fragment file by performing the following steps:
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1075
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1076 - 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.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1077
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1078 - Deduplicate: Sort the reads by cell barcodes and remove duplicated reads for each unique cell barcode.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1079
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1080 - Output: Convert BAM records to fragments (if paired-end) or single-end reads.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1081
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1082 The bam file needn’t be sorted or filtered.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1083
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1084 More details on the `SnapATAC2 documentation
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1085 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.make_fragment_file.html>`__
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1086
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1087 Generate cell by bin count matrix, using `pp.import_fragments`
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1088 ==============================================================
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1089
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1090 Import data fragment files and compute basic QC metrics.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1091
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1092 This function is used to generate and add a cell by bin count matrix to the AnnData object.
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1093 This function accepts both single-end and paired-end reads. If the records in the fragment file contain 6 columns with the last column representing the strand of the fragment, the fragments are considered single-ended. Otherwise, the fragments are considered paired-ended.
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1094
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1095 More details on the `SnapATAC2 documentation
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1096 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.import_fragments.html>`__
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1097
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1098 Generate cell by bin count matrix, using `pp.import_contacts`
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1099 =============================================================
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1100
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1101 Import chromatin contacts.
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1102
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1103 More details on the `SnapATAC2 documentation
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1104 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.import_contacts.html>`__
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1105
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1106 Generate cell by bin count matrix, using `pp.add_tile_matrix`
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1107 =============================================================
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1108
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1109 Generate cell by bin count matrix.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1110
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1111 This function is used to generate and add a cell by bin count matrix to the AnnData object.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1112
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1113 More details on the `SnapATAC2 documentation
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1114 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.add_tile_matrix.html>`__
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1115
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1116 Generate cell by gene activity matrix, using `pp.make_gene_matrix`
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1117 ==================================================================
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1118
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1119 Generate cell by gene activity matrix.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1120
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1121 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.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1122
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1123 More details on the `SnapATAC2 documentation
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1124 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.make_gene_matrix.html>`__
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1125
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1126 Filter cell outliers based on counts and numbers of genes expressed, using `pp.filter_cells`
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1127 ============================================================================================
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1128
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1129 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.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1130
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1131 More details on the `SnapATAC2 documentation
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1132 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.filter_cells.html>`__
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1133
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1134 Perform feature selection, using `pp.select_features`
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1135 =====================================================
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1136
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1137 Perform feature selection by selecting the most accessible features across all cells unless `max_iter` > 1
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1138
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1139 More details on the `SnapATAC2 documentation
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1140 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.select_features.html>`__
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1141
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1142 Compute probability of being a doublet using the scrublet algorithm, using `pp.scrublet`
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1143 ========================================================================================
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1144
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1145 Compute probability of being a doublet using the scrublet algorithm.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1146
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1147 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.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1148
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1149 More details on the `SnapATAC2 documentation
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1150 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.scrublet.html>`__
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1151
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1152 Remove doublets according to the doublet probability or doublet score, using `pp.filter_doublets`
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1153 =================================================================================================
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1154
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1155 Remove doublets according to the doublet probability or doublet score.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1156
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1157 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.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1158
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1159 More details on the `SnapATAC2 documentation
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1160 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.filter_doublets.html>`__
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1161
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1162 A modified MNN-Correct algorithm based on cluster centroid, using `pp.mnc_correct`
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1163 ==================================================================================
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1164
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1165 A modified MNN-Correct algorithm based on cluster centroid.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1166
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1167 More details on the `SnapATAC2 documentation
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1168 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.mnc_correct.html>`__
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1169
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1170 Use harmonypy to integrate different experiments,using `pp.harmony`
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1171 ===================================================================
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1172
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1173 Use harmonypy to integrate different experiments.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1174
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1175 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.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1176
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1177 More details on the `SnapATAC2 documentation
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1178 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.harmony.html>`__
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1179
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1180 Use Scanorama to integrate different experiments, using `pp.scanorama_integrate`
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1181 ================================================================================
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1182
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1183 Use Scanorama to integrate different experiments.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1184
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1185 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.
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1186
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1187 More details on the `SnapATAC2 documentation
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1188 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.scanorama_integrate.html>`__
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1189
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1190 Export fragments for each group of cells, using `ex.export_fragments`
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1191 =====================================================================
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1192
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 5
diff changeset
1193 Export and save fragments for a group of cells in a BED format file.
0
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1194
00a6721e1f81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
iuc
parents:
diff changeset
1195 More details on the `SnapATAC2 documentation
6
20c4011e1458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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1196 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.ex.export_fragments.html>`__
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1197
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1198 Export fragments for each group of cells, using `ex.export_coverage`
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1199 =====================================================================
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1200
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1201 Export and save coverage for a group of cells in a bedgraph or bigwig format file.
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1202
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1203 More details on the `SnapATAC2 documentation
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1204 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.ex.export_coverage.html>`__
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1205
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1206 ]]></help>
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1207 <expand macro="citations"/>
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1208 </tool>