Mercurial > repos > iuc > snapatac2_preprocessing

annotate preprocessing.xml @ 4:20d723aaa07c 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 16:39:37 +0000
parents 3d1103801ff2
children
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b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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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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23
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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',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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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',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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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',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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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
4
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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
4
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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,
0
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107 sorted_by_barcode = $method.sorted_by_barcode,
4
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108 bin_size = $method.bin_size,
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109 chunk_size = $method.chunk_size,
4
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110 tempdir = ".",
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111 backend = 'hdf5'
0
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112 )
4
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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(
0
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124 adata,
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125 bin_size = $method.bin_size,
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126 inplace = True,
0
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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 = $method.max_frag_size,
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137 #end if
1
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138 counting_strategy = '$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
4
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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(
0
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146 adata,
4
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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 = $method.include_gene_body,
0
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159 transcript_name_key = '$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 = $method.max_frag_size,
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168 #end if
1
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169 counting_strategy = '$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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diff changeset
173 snap.pp.filter_cells(
0
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parents:
diff changeset
174 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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175 min_counts = $method.min_counts,
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176 min_tsse = $method.min_tsse,
4
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177 #if str($method.max_counts) != '':
0
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178 max_counts = $method.max_counts,
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179 #end if
4
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180 #if str($method.max_tsse) != '':
0
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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))
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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185 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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186
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diff changeset
187 #else if $method.method == 'pp.select_features'
4
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diff changeset
188 snap.pp.select_features(
0
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iuc
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189 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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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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iuc
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201 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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202 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
203
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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204 #else if $method.method == 'pp.scrublet'
4
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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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diff changeset
214 snap.pp.scrublet(
0
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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,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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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))
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229 )
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230
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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231 #else if $method.method == 'pp.filter_doublets'
4
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232 snap.pp.filter_doublets(
0
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233 adata,
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diff changeset
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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diff changeset
239 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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240 inplace = True,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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241 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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242 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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243
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244 #else if $method.method == 'pp.mnc_correct'
4
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diff changeset
245 snap.pp.mnc_correct(
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
246 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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247 batch = '$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,
4
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diff changeset
251 @CONF_PARAMS_DATA_INTEGRATION@
0
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252 inplace = True,
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253 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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254 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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255
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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parents:
diff changeset
256 #else if $method.method == 'pp.harmony'
4
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diff changeset
257 snap.pp.harmony(
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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parents:
diff changeset
258 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
259 batch = '$method.batch',
4
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diff changeset
260 @CONF_PARAMS_DATA_INTEGRATION@
0
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iuc
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261 inplace = True
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262 )
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263
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264 #else if $method.method == 'pp.scanorama_integrate'
4
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265 snap.pp.scanorama_integrate(
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266 adata,
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267 batch = '$method.batch',
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268 n_neighbors = $method.n_neighbors,
4
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269 @CONF_PARAMS_DATA_INTEGRATION@
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270 inplace = True
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271 )
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272
4
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273 #else if $method.method == 'ex.export_fragments'
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274 snap.ex.export_fragments(
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275 adata,
4
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276 groupby = '$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
4
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288 #else if $method.method == 'ex.export_coverage'
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289 snap.ex.export_coverage(
0
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290 adata,
4
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291 groupby = '$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 = '.',
0
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323 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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324 )
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325 #end if
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326
4
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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
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330 ]]></configfile>
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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>
4
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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>
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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``"/>
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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">
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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"/>
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387 <expand macro="param_chunk_size" size="2000"/>
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388 </when>
4
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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>
4
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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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parents: 3
diff changeset
427 <param argument="downstream" type="integer" value="0" label="Number of base pairs downstream of regulatory domain"/>
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parents: 3
diff changeset
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
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
429 <param argument="transcript_name_key" type="text" value="transcript_name" label="The key of the transcript name in the gene annotation file"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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parents:
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"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
431 <param argument="gene_name_key" type="text" value="gene_name" label="The key of the gene name in the gene annotation file"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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parents:
diff changeset
432 <param argument="gene_id_key" type="text" value="gene_id" label="The key of the gene id in the gene annotation file"/>
4
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parents: 3
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433 <expand macro="param_min_max_frag_size"/>
1
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parents: 0
diff changeset
434 <expand macro="param_counting_strategy"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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parents:
diff changeset
435 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
436 <when value="pp.filter_cells">
4
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iuc
parents: 3
diff changeset
437 <expand macro="param_inputs_anndata"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
438 <param argument="min_counts" type="integer" value="1000" label="Minimum number of counts required for a cell to pass filtering"/>
4
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parents: 3
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
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
440 <param argument="max_counts" type="integer" value="" optional="true" label="Maximum number of counts required for a cell to pass filtering"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
441 <param argument="max_tsse" type="float" value="" optional="true" label="Maximum TSS enrichment score expressed required for a cell to pass filtering"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
442 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
443 <when value="pp.select_features">
4
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iuc
parents: 3
diff changeset
444 <expand macro="param_inputs_anndata"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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445 <param argument="n_features" type="integer" min="1" value="500000" label="Number of features to keep"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
446 <param argument="filter_lower_quantile" type="float" min="0" value="0.005" label="Lower quantile of the feature count distribution to filter out"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
447 <param argument="filter_upper_quantile" type="float" min="0" value="0.005" label="Upper quantile of the feature count distribution to filter out"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
448 <param argument="whitelist" type="data" format="bed" optional="true" label="A user provided bed file containing genome-wide whitelist regions"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
449 <param argument="blacklist" type="data" format="bed" optional="true" label="A user provided bed file containing genome-wide blacklist regions"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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parents:
diff changeset
450 <param argument="max_iter" type="integer" value="1" label="If greater than 1, this function will perform iterative clustering and feature selection"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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451 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
452 <when value="pp.scrublet">
4
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parents: 3
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453 <expand macro="param_inputs_anndata"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
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."/>
4
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parents: 3
diff changeset
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
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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parents:
diff changeset
456 <param argument="sim_doublet_ratio" type="float" value="2.0" label="Number of doublets to simulate relative to the number of observed cells"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
457 <param argument="expected_doublet_rate" type="float" value="0.1" label="Expected doublet rate"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
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"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
459 <param argument="use_approx_neighbors" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Whether to use approximate search"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
460 <param argument="random_state" type="integer" value="0" label="Random state"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
461 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
462 <when value="pp.filter_doublets">
4
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iuc
parents: 3
diff changeset
463 <expand macro="param_inputs_anndata"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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parents:
diff changeset
464 <param argument="probability_threshold" type="float" value="0.5" label="Threshold for doublet probability"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
465 <param argument="score_threshold" type="float" value="" optional="true" label="Threshold for doublet score"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
466 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
467 <when value="pp.mnc_correct">
4
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iuc
parents: 3
diff changeset
468 <expand macro="param_inputs_anndata"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
469 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
470 <expand macro="sanitize_query"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
471 </param>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
472 <param argument="n_neighbors" type="integer" value="5" label="Number of mutual nearest neighbors"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
473 <param argument="n_clusters" type="integer" value="40" label="Number of clusters"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
474 <param argument="n_iter" type="integer" value="1" label="Number of iterations"/>
4
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parents: 3
diff changeset
475 <expand macro="param_data_integration"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
476 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
477 <when value="pp.harmony">
4
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parents: 3
diff changeset
478 <expand macro="param_inputs_anndata"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
479 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
480 <expand macro="sanitize_query"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
481 </param>
4
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parents: 3
diff changeset
482 <expand macro="param_data_integration"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
483 </when>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
484 <when value="pp.scanorama_integrate">
4
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parents: 3
diff changeset
485 <expand macro="param_inputs_anndata"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
486 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
487 <expand macro="sanitize_query"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
488 </param>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
489 <param argument="n_neighbors" type="integer" value="20" label="Number of mutual nearest neighbors"/>
4
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parents: 3
diff changeset
490 <expand macro="param_data_integration"/>
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diff changeset
491 </when>
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iuc
parents: 3
diff changeset
492 <when value="ex.export_fragments">
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iuc
parents: 3
diff changeset
493 <expand macro="param_inputs_anndata"/>
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iuc
parents: 3
diff changeset
494 <expand macro="param_groupby"/>
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parents: 3
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"/>
20d723aaa07c 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
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
497 </when>
4
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parents: 3
diff changeset
498 <when value="ex.export_coverage">
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iuc
parents: 3
diff changeset
499 <expand macro="param_inputs_anndata"/>
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iuc
parents: 3
diff changeset
500 <expand macro="param_groupby"/>
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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"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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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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parents: 3
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>
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505 <option value="None">No normalization</option>
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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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507 <option value="BPM">BPM (per bin) = #reads per bin / sum of all reads per bin (in millions)</option>
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508 </param>
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509 <param argument="--include_for_norm" type="data" format="bed" optional="true" label="A BED file containing the genomic loci to include for normalization"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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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"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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511 <param argument="--min_frag_length" type="integer" optional="true" min="0" value="" label="Minimum fragment length to be included in the computation"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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512 <param argument="--max_frag_length" type="integer" min="0" value="2000" label="Maximum fragment length to be included in the computation"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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diff changeset
513 <param argument="--counting_strategy" type="select" label="The strategy to compute feature counts">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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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>
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515 <option value="insertion">insertion - the feature counts are assigned based on the number of insertions that overlap with a region of interest</option>
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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>
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517 </param>
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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"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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519 <param argument="--output_format" type="select" label="The output format">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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520 <option value="bigwig" selected="true">bigwig</option>
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521 <option value="bedgraph">bedgraph</option>
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522 </param>
0
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523 </when>
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524 </conditional>
4
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diff changeset
525 <expand macro="param_common_advanced"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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526 </inputs>
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iuc
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diff changeset
527 <outputs>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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528 <data name="fragments_out" format="interval" label="${tool.name} (${method.method}) on ${on_string}: Fragment file">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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529 <filter>method['method'] == 'pp.make_fragment_file'</filter>
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530 </data>
4
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531 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad.gz" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
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532 <filter>method['method'] != 'pp.make_fragment_file' and method['method'] != 'ex.export_fragments' and method['method'] != 'ex.export_coverage'</filter>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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diff changeset
533 <change_format>
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iuc
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diff changeset
534 <when input="method.method" value="pp.import_fragments" format="h5" />
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
535 </change_format>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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536 </data>
4
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537 <collection name="export_fragment" type="list" format="bed" label="${tool.name} (${method.method}) on ${on_string}: exported fragments">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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diff changeset
538 <discover_datasets pattern="__name_and_ext__" directory="fragments"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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diff changeset
539 <filter>method['method'] == 'ex.export_fragments'</filter>
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540 </collection>
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iuc
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diff changeset
541 <collection name="export_coverage" type="list" label="${tool.name} (${method.method}) on ${on_string}: exported coverage">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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diff changeset
542 <discover_datasets pattern="__name_and_ext__" directory="coverage"/>
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diff changeset
543 <filter>method['method'] == 'ex.export_coverage'</filter>
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544 </collection>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
545 <data name="hidden_output" format="txt" label="Log file">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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546 <filter>advanced_common['show_log']</filter>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
547 </data>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
548 </outputs>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
549 <tests>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
550 <test expect_num_outputs="1">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
551 <!-- pp.make_fragment_file -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
552 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
553 <param name="method" value="pp.make_fragment_file"/>
4
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parents: 3
diff changeset
554 <param name="bam_file" location="https://zenodo.org/records/17512085/files/pbmc_500_chr21_subsample.bam"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
555 <param name="is_paired" value="true"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
556 <conditional name="barcode">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
557 <param name="extract_type" value="from_tag"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
558 <param name="barcode_tag" value="CB"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
559 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
560 <param name="shift_left" value="4"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
561 <param name="shift_right" value="-5"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
562 <param name="min_mapq" value="10"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
563 <param name="chunk_size" value="50000000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
564 </conditional>
4
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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
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
566 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
567 <test expect_num_outputs="2">
4
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parents: 3
diff changeset
568 <!-- pp.import_fragments -->
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
569 <conditional name="method">
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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parents: 3
diff changeset
570 <param name="method" value="pp.import_fragments"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
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parents: 3
diff changeset
571 <param name="fragment_file" location="https://zenodo.org/records/17512085/files/pp.make_fragment_file.pbmc_500_chr21.tsv.gz"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
572 <param name="chrom_sizes" location="https://zenodo.org/records/17512085/files/chrom_size.tabular"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
573 <param name="min_num_fragments" value="200"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
574 <param name="sorted_by_barcode" value="true"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
575 <param name="chrM" value="" />
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
576 <param name="shift_left" value="0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
577 <param name="shift_right" value="0"/>
4
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iuc
parents: 3
diff changeset
578 <param name="chunk_size" value="2000"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
579 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
580 <section name="advanced_common">
4
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iuc
parents: 3
diff changeset
581 <param name="show_log" value="true" />
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
582 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
583 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
584 <assert_contents>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
585 <has_text_matching expression="snap.pp.import_fragments"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
586 <has_text_matching expression="chrom_sizes"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
587 <has_text_matching expression="shift_left = 0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
588 <has_text_matching expression="shift_right = 0"/>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
589 <has_text_matching expression="chunk_size = 2000"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
590 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
591 </output>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
592 <output name="anndata_out" ftype="h5">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
593 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
594 <has_h5_keys keys="obs/n_fragment,obs/frac_dup,obs/frac_mito"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
595 <has_h5_keys keys="uns/reference_sequences"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
596 <has_h5_keys keys="obsm/fragment_paired"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
597 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
598 </output>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
599 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
600 <test expect_num_outputs="2">
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
601 <!-- pp.make_gene_matrix - history -->
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
602 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
603 <param name="method" value="pp.make_gene_matrix"/>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
604 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
605 <conditional name="gff_file_condi">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
606 <param name="gffSource" value="history"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
607 <param name="gff_history" location="https://zenodo.org/records/17512085/files/chr21.gff3.gz"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
608 </conditional>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
609 <param name="chunk_size" value="500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
610 <param name="use_x" value="False"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
611 <param name="id_type" value="gene"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
612 <param name="transcript_name_key" value="transcript_name"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
613 <param name="transcript_id_key" value="transcript_id"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
614 <param name="gene_name_key" value="gene_name"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
615 <param name="gene_id_key" value="gene_id"/>
1
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
616 <param name="counting_strategy" value="insertion"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
617 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
618 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
619 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
620 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
621 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
622 <assert_contents>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
623 <has_text_matching expression="snap.pp.make_gene_matrix"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
624 <has_text_matching expression="chunk_size = 500"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
625 <has_text_matching expression="use_x = False"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
626 <has_text_matching expression="id_type = 'gene'"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
627 <has_text_matching expression="transcript_name_key = 'transcript_name'"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
628 <has_text_matching expression="transcript_id_key = 'transcript_id'"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
629 <has_text_matching expression="gene_name_key = 'gene_name'"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
630 <has_text_matching expression="gene_id_key = 'gene_id'"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
631 <has_text_matching expression="counting_strategy = 'insertion'"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
632 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
633 </output>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
634 <output name="anndata_out" ftype="h5ad">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
635 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
636 <has_h5_keys keys="obs/n_fragment,obs/frac_dup,obs/tsse"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
637 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
638 </output>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
639 </test>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
640 <test expect_num_outputs="2">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
641 <!-- pp.make_gene_matrix - cached -->
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
642 <conditional name="method">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
643 <param name="method" value="pp.make_gene_matrix"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
644 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
645 <conditional name="gff_file_condi">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
646 <param name="gffSource" value="cached"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
647 <param name="gff_pre_installed" value="hg38"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
648 </conditional>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
649 <param name="chunk_size" value="500"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
650 <param name="use_x" value="False"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
651 <param name="id_type" value="gene"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
652 <param name="transcript_name_key" value="transcript_name"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
653 <param name="transcript_id_key" value="transcript_id"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
654 <param name="gene_name_key" value="gene_name"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
655 <param name="gene_id_key" value="gene_id"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
656 <param name="counting_strategy" value="insertion"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
657 </conditional>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
658 <section name="advanced_common">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
659 <param name="show_log" value="true" />
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
660 </section>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
661 <output name="hidden_output">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
662 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
663 <has_text_matching expression="snap.pp.make_gene_matrix"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
664 <has_text_matching expression="chunk_size = 500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
665 <has_text_matching expression="use_x = False"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
666 <has_text_matching expression="id_type = 'gene'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
667 <has_text_matching expression="transcript_name_key = 'transcript_name'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
668 <has_text_matching expression="transcript_id_key = 'transcript_id'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
669 <has_text_matching expression="gene_name_key = 'gene_name'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
670 <has_text_matching expression="gene_id_key = 'gene_id'"/>
1
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
671 <has_text_matching expression="counting_strategy = 'insertion'"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
672 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
673 </output>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
674 <output name="anndata_out" ftype="h5ad">
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
675 <assert_contents>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
676 <has_h5_keys keys="obs/n_fragment,obs/frac_dup,obs/tsse"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
677 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
678 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
679 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
680 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
681 <!-- pp.filter_cells -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
682 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
683 <param name="method" value="pp.filter_cells"/>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
684 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
685 <param name="min_counts" value="500"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
686 <param name="min_tsse" value="1"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
687 <param name="max_counts" value="10000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
688 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
689 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
690 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
691 </section>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
692 <assert_stdout>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
693 <has_text_matching expression="6 × 9342"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
694 </assert_stdout>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
695 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
696 <assert_contents>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
697 <has_text_matching expression="snap.pp.filter_cells"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
698 <has_text_matching expression="min_counts = 500"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
699 <has_text_matching expression="min_tsse = 1"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
700 <has_text_matching expression="max_counts = 10000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
701 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
702 </output>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
703 <output name="anndata_out" ftype="h5ad">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
704 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
705 <has_h5_keys keys="obs/n_fragment"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
706 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
707 </output>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
708 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
709 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
710 <!-- pp.add_tile_matrix -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
711 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
712 <param name="method" value="pp.add_tile_matrix"/>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
713 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
714 <param name="bin_size" value="5000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
715 <param name="chunk_size" value="500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
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"/>
1
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
717 <param name="counting_strategy" value="insertion"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
718 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
719 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
720 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
721 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
722 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
723 <assert_contents>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
724 <has_text_matching expression="snap.pp.add_tile_matrix"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
725 <has_text_matching expression="bin_size = 5000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
726 <has_text_matching expression="chunk_size = 500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
727 <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
1
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
728 <has_text_matching expression="counting_strategy = 'insertion'"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
729 </assert_contents>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
730 </output>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
731 <output name="anndata_out" ftype="h5ad">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
732 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
733 <has_h5_keys keys="obs/n_fragment,obs/frac_dup,obs/frac_mito,obs/tsse"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
734 <has_h5_keys keys="uns/reference_sequences"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
735 <has_h5_keys keys="obsm/fragment_paired"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
736 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
737 </output>
1
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
738 </test>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
739 <test expect_num_outputs="2">
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
740 <!-- pp.add_tile_matrix counting_strategy fragment -->
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
741 <conditional name="method">
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
742 <param name="method" value="pp.add_tile_matrix"/>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
743 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
1
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
744 <param name="bin_size" value="5000"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
745 <param name="chunk_size" value="500"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
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"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
747 <param name="counting_strategy" value="fragment"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
748 </conditional>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
749 <section name="advanced_common">
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
750 <param name="show_log" value="true" />
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
751 </section>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
752 <output name="hidden_output">
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
753 <assert_contents>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
754 <has_text_matching expression="snap.pp.add_tile_matrix"/>
1
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
755 <has_text_matching expression="bin_size = 5000"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
756 <has_text_matching expression="chunk_size = 500"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
757 <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
758 <has_text_matching expression="counting_strategy = 'fragment'"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
759 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
760 </output>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
761 <output name="anndata_out" ftype="h5ad">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
762 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
763 <has_h5_keys keys="obs/n_fragment,obs/frac_dup,obs/tsse"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
764 <has_h5_keys keys="obsm/fragment_paired"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
765 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
766 </output>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
767 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
768 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
769 <!-- pp.select_features -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
770 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
771 <param name="method" value="pp.select_features"/>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
772 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
773 <param name="n_features" value="15000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
774 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
775 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
776 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
777 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
778 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
779 <assert_contents>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
780 <has_text_matching expression="snap.pp.select_features"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
781 <has_text_matching expression="n_features = 15000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
782 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
783 </output>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
784 <output name="anndata_out" ftype="h5ad">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
785 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
786 <has_h5_keys keys="var/count,var/selected"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
787 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
788 </output>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
789 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
790 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
791 <!-- pp.scrublet -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
792 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
793 <param name="method" value="pp.scrublet"/>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
794 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.select_features.pbmc_500_chr21.h5ad"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
795 <param name="n_comps" value="15"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
796 <param name="sim_doublet_ratio" value="2.0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
797 <param name="expected_doublet_rate" value="0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
798 <param name="random_state" value="0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
799 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
800 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
801 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
802 </section>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
803 <assert_stdout>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
804 <has_text_matching expression="158 × 9342"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
805 </assert_stdout>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
806 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
807 <assert_contents>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
808 <has_text_matching expression="snap.pp.scrublet"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
809 <has_text_matching expression="n_comps = 15"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
810 <has_text_matching expression="sim_doublet_ratio = 2.0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
811 <has_text_matching expression="expected_doublet_rate = 0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
812 <has_text_matching expression="random_state = 0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
813 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
814 </output>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
815 <output name="anndata_out" ftype="h5ad">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
816 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
817 <has_h5_keys keys="obs/doublet_probability,obs/doublet_score"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
818 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
819 </output>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
820 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
821 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
822 <!-- pp.filter_doublets -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
823 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
824 <param name="method" value="pp.filter_doublets"/>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
825 <param name="adata" location="https://zenodo.org/records/17512085/files/pp.scrublet.pbmc_500_chr21.h5ad"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
826 <param name="probability_threshold" value="0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
827 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
828 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
829 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
830 </section>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
831 <assert_stdout>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
832 <has_text_matching expression="156 × 9342"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
833 </assert_stdout>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
834 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
835 <assert_contents>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
836 <has_text_matching expression="snap.pp.filter_doublets"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
837 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
838 </output>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
839 <output name="anndata_out" ftype="h5ad">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
840 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
841 <has_h5_keys keys="obs/doublet_probability,obs/doublet_score"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
842 <has_h5_keys keys="uns/doublet_rate"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
843 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
844 </output>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
845 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
846 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
847 <!-- pp.mnc_correct -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
848 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
849 <param name="method" value="pp.mnc_correct"/>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
850 <param name="adata" location="https://zenodo.org/records/17512085/files/pbmc_500_chr21.batch.h5ad"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
851 <param name="batch" value="batch"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
852 <param name="n_neighbors" value="3"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
853 <param name="n_clusters" value="10"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
854 <param name="use_rep" value="X_spectral"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
855 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
856 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
857 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
858 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
859 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
860 <assert_contents>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
861 <has_text_matching expression="snap.pp.mnc_correct"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
862 <has_text_matching expression="batch = 'batch'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
863 <has_text_matching expression="n_neighbors = 3"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
864 <has_text_matching expression="n_clusters = 10"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
865 <has_text_matching expression="batch = 'batch'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
866 <has_text_matching expression="use_rep = 'X_spectral'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
867 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
868 </output>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
869 <output name="anndata_out" ftype="h5ad">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
870 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
871 <has_h5_keys keys="obsm/X_spectral_mnn"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
872 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
873 </output>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
874 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
875 <test expect_num_outputs="2">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
876 <!-- pp.harmony -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
877 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
878 <param name="method" value="pp.harmony"/>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
879 <param name="adata" location="https://zenodo.org/records/17512085/files/pbmc_500_chr21.batch.h5ad"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
880 <param name="batch" value="batch"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
881 <param name="use_rep" value="X_spectral"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
882 </conditional>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
883 <section name="advanced_common">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
884 <param name="show_log" value="true" />
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
885 </section>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
886 <output name="hidden_output">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
887 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
888 <has_text_matching expression="snap.pp.harmony"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
889 <has_text_matching expression="batch = 'batch'"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
890 <has_text_matching expression="use_rep = 'X_spectral'"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
891 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
892 </output>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
893 <output name="anndata_out" ftype="h5ad">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
894 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
895 <has_h5_keys keys="obsm/X_spectral_harmony"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
896 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
897 </output>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
898 </test>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
899 <test expect_num_outputs="2">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
900 <!-- pp.scanorama_integrate -->
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
901 <conditional name="method">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
902 <param name="method" value="pp.scanorama_integrate"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
903 <param name="adata" location="https://zenodo.org/records/17512085/files/pbmc_500_chr21.batch.h5ad"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
904 <param name="batch" value="batch"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
905 <param name="use_rep" value="X_spectral"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
906 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
907 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
908 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
909 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
910 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
911 <assert_contents>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
912 <has_text_matching expression="snap.pp.scanorama_integrate"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
913 <has_text_matching expression="batch = 'batch'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
914 <has_text_matching expression="use_rep = 'X_spectral'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
915 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
916 </output>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
917 <output name="anndata_out" ftype="h5ad">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
918 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
919 <has_h5_keys keys="obsm/X_spectral_scanorama"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
920 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
921 </output>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
922 </test>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
923 <!-- pp.import_contacts -->
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
924 <test expect_num_outputs="2">
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
925 <conditional name="method">
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
926 <param name="method" value="pp.import_contacts"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
927 <param name="contact_file" location="https://zenodo.org/records/17512085/files/pp.make_fragment_file.pbmc_500_chr21.tsv.gz"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
928 <param name="chrom_sizes" location="https://zenodo.org/records/17512085/files/chrom_size.tabular"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
929 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
930 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
931 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
932 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
933 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
934 <assert_contents>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
935 <has_text_matching expression="snap.pp.import_contacts"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
936 <has_text_matching expression="chrom_sizes"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
937 <has_text_matching expression="sorted_by_barcode = True"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
938 <has_text_matching expression="bin_size = 500000"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
939 <has_text_matching expression="chunk_size = 200"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
940 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
941 </output>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
942 <output name="anndata_out" ftype="h5ad">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
943 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
944 <has_h5_keys keys="uns/reference_sequences"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
945 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
946 </output>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
947 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
948 <test expect_num_outputs="2">
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
949 <!-- ex.export_fragments -->
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
950 <conditional name="method">
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
951 <param name="method" value="ex.export_fragments"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
952 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
953 <param name="groupby" value="leiden"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
954 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
955 <section name="advanced_common">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
956 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
957 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
958 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
959 <assert_contents>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
960 <has_text_matching expression="snap.ex.export_fragments"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
961 <has_text_matching expression="groupby = &apos;leiden&apos;"/>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
962 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
963 </output>
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
964 <output_collection name="export_fragment" type="list" count="8">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
965 <element name="-1.bed">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
966 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
967 <has_n_lines n="1018"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
968 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
969 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
970 <element name="0.bed">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
971 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
972 <has_n_lines n="2973"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
973 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
974 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
975 <element name="1.bed">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
976 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
977 <has_n_lines n="1661"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
978 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
979 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
980 <element name="2.bed">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
981 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
982 <has_n_lines n="1605"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
983 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
984 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
985 <element name="3.bed">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
986 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
987 <has_n_lines n="1457"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
988 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
989 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
990 <element name="4.bed">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
991 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
992 <has_n_lines n="620"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
993 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
994 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
995 <element name="5.bed">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
996 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
997 <has_n_lines n="2618"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
998 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
999 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1000 <element name="6.bed">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1001 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1002 <has_n_lines n="225"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1003 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1004 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1005 </output_collection>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1006 </test>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1007 <test expect_num_outputs="2">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1008 <!-- ex.export_coverage -->
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1009 <conditional name="method">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1010 <param name="method" value="ex.export_coverage"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1011 <param name="adata" location="https://zenodo.org/records/17512085/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1012 <param name="groupby" value="leiden"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1013 </conditional>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1014 <section name="advanced_common">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1015 <param name="show_log" value="true" />
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1016 </section>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1017 <output name="hidden_output">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1018 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1019 <has_text_matching expression="snap.ex.export_coverage"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1020 <has_text_matching expression="groupby = &apos;leiden&apos;"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1021 <has_text_matching expression="output_format = &apos;bigwig&apos;"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1022 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1023 </output>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1024 <output_collection name="export_coverage" type="list" count="8">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1025 <element name="-1">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1026 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1027 <has_n_lines n="981"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1028 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1029 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1030 <element name="0">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1031 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1032 <has_n_lines n="2447"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1033 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1034 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1035 <element name="1">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1036 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1037 <has_n_lines n="1571"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1038 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1039 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1040 <element name="2">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1041 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1042 <has_n_lines n="1499"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1043 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1044 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1045 <element name="3">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1046 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1047 <has_n_lines n="1269"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1048 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1049 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1050 <element name="4">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1051 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1052 <has_n_lines n="640"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1053 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1054 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1055 <element name="5">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1056 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1057 <has_n_lines n="2420"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1058 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1059 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1060 <element name="6">
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1061 <assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1062 <has_n_lines n="177"/>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1063 </assert_contents>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1064 </element>
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1065 </output_collection>
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1066 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1067 </tests>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1068 <help><![CDATA[
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1069 Convert a BAM file to a fragment file, using `pp.make_fragment_file`
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1070 ====================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1071
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1072 Convert a BAM file to a fragment file.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1073
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1074 Convert a BAM file to a fragment file by performing the following steps:
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1075
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1077
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1078 - Deduplicate: Sort the reads by cell barcodes and remove duplicated reads for each unique cell barcode.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1079
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1080 - Output: Convert BAM records to fragments (if paired-end) or single-end reads.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1081
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1082 The bam file needn’t be sorted or filtered.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1083
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1084 More details on the `SnapATAC2 documentation
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1085 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.make_fragment_file.html>`__
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1086
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1087 Generate cell by bin count matrix, using `pp.import_fragments`
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1088 ==============================================================
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1089
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1090 Import data fragment files and compute basic QC metrics.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1091
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1092 This function is used to generate and add a cell by bin count matrix to the AnnData object.
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
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
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1094
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1095 More details on the `SnapATAC2 documentation
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
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diff changeset
1096 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.import_fragments.html>`__
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1097
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iuc
parents: 3
diff changeset
1098 Generate cell by bin count matrix, using `pp.import_contacts`
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1099 =============================================================
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1100
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1101 Import chromatin contacts.
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iuc
parents: 3
diff changeset
1102
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iuc
parents: 3
diff changeset
1103 More details on the `SnapATAC2 documentation
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1104 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.import_contacts.html>`__
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1105
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1106 Generate cell by bin count matrix, using `pp.add_tile_matrix`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1107 =============================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1108
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1109 Generate cell by bin count matrix.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1110
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1111 This function is used to generate and add a cell by bin count matrix to the AnnData object.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1112
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1113 More details on the `SnapATAC2 documentation
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1114 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.add_tile_matrix.html>`__
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1115
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1116 Generate cell by gene activity matrix, using `pp.make_gene_matrix`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1117 ==================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1118
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1119 Generate cell by gene activity matrix.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1120
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1122
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1123 More details on the `SnapATAC2 documentation
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1124 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.make_gene_matrix.html>`__
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1125
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1126 Filter cell outliers based on counts and numbers of genes expressed, using `pp.filter_cells`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1127 ============================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1128
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1130
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1131 More details on the `SnapATAC2 documentation
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1132 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.filter_cells.html>`__
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1133
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1134 Perform feature selection, using `pp.select_features`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1135 =====================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1136
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1137 Perform feature selection by selecting the most accessible features across all cells unless `max_iter` > 1
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1138
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1139 More details on the `SnapATAC2 documentation
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1140 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.select_features.html>`__
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1141
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1142 Compute probability of being a doublet using the scrublet algorithm, using `pp.scrublet`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1143 ========================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1144
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1145 Compute probability of being a doublet using the scrublet algorithm.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1146
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1148
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1149 More details on the `SnapATAC2 documentation
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1150 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.scrublet.html>`__
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1151
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1152 Remove doublets according to the doublet probability or doublet score, using `pp.filter_doublets`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1153 =================================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1154
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1155 Remove doublets according to the doublet probability or doublet score.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1156
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1158
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1159 More details on the `SnapATAC2 documentation
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1160 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.filter_doublets.html>`__
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1161
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1162 A modified MNN-Correct algorithm based on cluster centroid, using `pp.mnc_correct`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1163 ==================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1164
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1165 A modified MNN-Correct algorithm based on cluster centroid.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1166
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1167 More details on the `SnapATAC2 documentation
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1168 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.mnc_correct.html>`__
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1169
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1170 Use harmonypy to integrate different experiments,using `pp.harmony`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1171 ===================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1172
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1173 Use harmonypy to integrate different experiments.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1174
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1176
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1177 More details on the `SnapATAC2 documentation
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1178 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.harmony.html>`__
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1179
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1180 Use Scanorama to integrate different experiments, using `pp.scanorama_integrate`
4
20d723aaa07c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 commit e0f59fae19e57f54ae0c351a16dd1805d12aba1d
iuc
parents: 3
diff changeset
1181 ================================================================================
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1182
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1183 Use Scanorama to integrate different experiments.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1184
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1186
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
1187 More details on the `SnapATAC2 documentation
4
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1188 <https://scverse.org/SnapATAC2/api/_autosummary/snapatac2.pp.scanorama_integrate.html>`__
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1189
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1190 Export fragments for each group of cells, using `ex.export_fragments`
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1191 =====================================================================
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1192
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1193 Export and save fragments for a group of cells in a BED format file.
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1194
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1195 More details on the `SnapATAC2 documentation
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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>