Mercurial > repos > iuc > snapatac2_preprocessing

annotate preprocessing.xml @ 1:e3b85e48487b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
author iuc
date Wed, 17 Jul 2024 05:54:26 +0000
parents b2844c6efb72
children 3d1103801ff2
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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@">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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2 <description>and integration</description>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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3 <macros>
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4 <import>macros.xml</import>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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5 </macros>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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6 <requirements>
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7 <expand macro="requirements"/>
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8 </requirements>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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9 <command detect_errors="exit_code"><![CDATA[
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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10 #if $method.method != 'pp.make_fragment_file' and $method.method != 'pp.import_data'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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11 @PREP_ADATA@
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12 #end if
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13 @CMD@
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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14 ]]></command>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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15 <configfiles>
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16 <configfile name="script_file"><![CDATA[
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17 @CMD_imports@
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18
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19 #if $method.method != 'pp.make_fragment_file' and $method.method != 'pp.import_data'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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20 @CMD_read_inputs@
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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21 #end if
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22
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23 #if $method.method == 'pp.make_fragment_file'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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24 sa.pp.make_fragment_file(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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25 bam_file = '$method.bam_file',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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26 is_paired = $method.is_paired,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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27 #if $method.barcode.extract_type == 'from_tag'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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28 #if $method.barcode.barcode_tag != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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29 barcode_tag = '$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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30 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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31 #elif $method.barcode.extract_type == 'from_read_names'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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32 #if $method.barcode.barcode_regex != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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33 barcode_regex = '$method.barcode.barcode_regex',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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34 #end if
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35 #end if
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36 #if $method.umi_tag != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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37 umi_tag = '$method.umi_tag',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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38 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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39 #if $method.umi_regex != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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40 umi_regex = '$method.umi_regex',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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41 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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42 shift_right = $method.shift_right,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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43 shift_left = $method.shift_left,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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44 min_mapq = $method.min_mapq,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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45 chunk_size = $method.chunk_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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46 compression = 'gzip',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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47 output_file = '$fragments_out',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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48 tempdir = "."
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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49 )
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50
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51 #else if $method.method == 'pp.import_data'
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52 import csv
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53 with open('$method.chrom_sizes') as f:
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54 chr_sizes = {x[0]:int(x[1]) for x in csv.reader(f, delimiter='\t')}
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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55
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56 sa.pp.import_data(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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57 fragment_file = '$method.fragment_file',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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58 chrom_sizes = chr_sizes,
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59 min_num_fragments = $method.min_num_fragments,
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60 sorted_by_barcode = $method.sorted_by_barcode,
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61 #if str($method.whitelist) != 'None'
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62 whitelist = '$method.whitelist',
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63 #end if
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64 shift_left = $method.shift_left,
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65 shift_right = $method.shift_right,
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66 #set $chr_mt = ([x.strip() for x in str($method.chrM).split(',')])
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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67 chrM = $chr_mt,
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68 chunk_size = $method.chunk_size,
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69 file = 'anndata.h5ad',
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70 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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71 )
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72
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73 #else if $method.method == 'pp.add_tile_matrix'
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74 sa.pp.add_tile_matrix(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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75 adata,
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76 bin_size = $method.bin_size,
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77 chunk_size = $method.chunk_size,
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78 #if $method.exclude_chroms != ''
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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79 #set $excl_chroms = ([x.strip() for x in str($method.exclude_chroms).split(',')])
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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80 exclude_chroms = $excl_chroms,
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81 #end if
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82 #if $method.min_frag_size
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83 min_frag_size = $method.min_frag_size,
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84 #end if
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diff changeset
85 #if $method.max_frag_size
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
86 max_frag_size = $method.max_frag_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
87 #end if
1
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
88 counting_strategy = '$method.counting_strategy',
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
89 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
90 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
91
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
92 #else if $method.method == 'pp.make_gene_matrix'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
93 adata = sa.pp.make_gene_matrix(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
94 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
95 gene_anno = '$method.gene_anno',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
96 chunk_size = $method.chunk_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
97 use_x = $method.use_x,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
98 id_type = '$method.id_type',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
99 transcript_name_key = '$method.transcript_name_key',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
100 transcript_id_key = '$method.transcript_id_key',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
101 gene_name_key = '$method.gene_name_key',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
102 gene_id_key = '$method.gene_id_key',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
103 #if $method.min_frag_size
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
104 min_frag_size = $method.min_frag_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
105 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
106 #if $method.max_frag_size
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
107 max_frag_size = $method.max_frag_size,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
108 #end if
1
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
109 counting_strategy = '$method.counting_strategy'
0
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
110 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
111
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
112 #else if $method.method == 'pp.filter_cells'
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
113 sa.pp.filter_cells(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
114 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
115 min_counts = $method.min_counts,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
116 min_tsse = $method.min_tsse,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
117 #if $method.max_counts
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
118 max_counts = $method.max_counts,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
119 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
120 #if $method.max_tsse
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iuc
parents:
diff changeset
121 max_tsse = $method.max_tsse,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
122 #end if
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iuc
parents:
diff changeset
123 inplace = True,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
124 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
125 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
126
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iuc
parents:
diff changeset
127 #else if $method.method == 'pp.select_features'
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iuc
parents:
diff changeset
128 sa.pp.select_features(
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iuc
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diff changeset
129 adata,
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iuc
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diff changeset
130 n_features = $method.n_features,
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iuc
parents:
diff changeset
131 filter_lower_quantile = $method.filter_lower_quantile,
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iuc
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132 filter_upper_quantile = $method.filter_upper_quantile,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
133 #if str($method.whitelist) != 'None'
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iuc
parents:
diff changeset
134 whitelist = '$method.whitelist',
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iuc
parents:
diff changeset
135 #end if
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
136 #if str($method.blacklist) != 'None'
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iuc
parents:
diff changeset
137 blacklist = '$method.blacklist',
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
138 #end if
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iuc
parents:
diff changeset
139 max_iter = $method.max_iter,
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iuc
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diff changeset
140 inplace = True,
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iuc
parents:
diff changeset
141 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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iuc
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diff changeset
142 )
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iuc
parents:
diff changeset
143
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iuc
parents:
diff changeset
144 #else if $method.method == 'pp.scrublet'
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iuc
parents:
diff changeset
145 sa.pp.scrublet(
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
146 adata,
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
147 #if $method.features
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diff changeset
148 features = '$method.features',
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diff changeset
149 #end if
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iuc
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diff changeset
150 n_comps = $method.n_comps,
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iuc
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151 sim_doublet_ratio = $method.sim_doublet_ratio,
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iuc
parents:
diff changeset
152 expected_doublet_rate = $method.expected_doublet_rate,
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diff changeset
153 #if $method.n_neighbors
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154 n_neighbors = $method.n_neighbors,
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parents:
diff changeset
155 #end if
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iuc
parents:
diff changeset
156 use_approx_neighbors = $method.use_approx_neighbors,
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iuc
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diff changeset
157 random_state = $method.random_state,
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158 inplace = True,
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iuc
parents:
diff changeset
159 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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iuc
parents:
diff changeset
160 )
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
161
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
162 #else if $method.method == 'pp.filter_doublets'
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iuc
parents:
diff changeset
163 sa.pp.filter_doublets(
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iuc
parents:
diff changeset
164 adata,
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iuc
parents:
diff changeset
165 #if $method.probability_threshold
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iuc
parents:
diff changeset
166 probability_threshold = $method.probability_threshold,
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iuc
parents:
diff changeset
167 #end if
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iuc
parents:
diff changeset
168 #if $method.score_threshold
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iuc
parents:
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169 score_threshold = $method.score_threshold,
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iuc
parents:
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170 #end if
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parents:
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171 inplace = True,
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iuc
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172 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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173 )
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174
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175 #else if $method.method == 'pp.mnc_correct'
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176 sa.pp.mnc_correct(
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177 adata,
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178 batch = '$method.batch',
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179 n_neighbors = $method.n_neighbors,
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180 n_clusters = $method.n_clusters,
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181 n_iter = $method.n_iter,
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182 @CMD_params_data_integration@
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183 inplace = True,
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184 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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185 )
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186
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187 #else if $method.method == 'pp.harmony'
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188 sa.pp.harmony(
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189 adata,
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190 batch = '$method.batch',
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191 @CMD_params_data_integration@
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192 inplace = True
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193 )
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194
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195 #else if $method.method == 'pp.scanorama_integrate'
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196 sa.pp.scanorama_integrate(
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197 adata,
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198 batch = '$method.batch',
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199 n_neighbors = $method.n_neighbors,
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200 @CMD_params_data_integration@
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201 inplace = True
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202 )
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203
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204 #else if $method.method == 'metrics.frag_size_distr'
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205 sa.metrics.frag_size_distr(
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206 adata,
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207 max_recorded_size = $method.max_recorded_size,
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208 add_key = '$method.add_key',
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209 inplace = True,
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210 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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211 )
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212
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213 #else if $method.method == 'metrics.tsse'
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214 sa.metrics.tsse(
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215 adata,
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216 gene_anno = '$method.gene_anno',
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217 inplace = True,
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218 n_jobs = int(os.getenv("GALAXY_SLOTS", 4))
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219 )
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220 #end if
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221
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222 #if $method.method != 'pp.make_fragment_file' and $method.method != 'pp.import_data'
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223 @CMD_anndata_write_outputs@
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224 #end if
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225 ]]></configfile>
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226 </configfiles>
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227 <inputs>
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228 <conditional name="method">
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229 <param name="method" type="select" label="Method used for preprocessing">
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230 <option value="pp.make_fragment_file">Convert a BAM file to a fragment file, using 'pp.make_fragment_file'</option>
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231 <option value="pp.import_data">Import data fragment files and compute basic QC metrics, using 'pp.import_data'</option>
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232 <option value="pp.add_tile_matrix">Generate cell by bin count matrix, using 'pp.add_tile_matrix'</option>
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233 <option value="pp.make_gene_matrix">Generate cell by gene activity matrix, using 'pp.make_gene_matrix'</option>
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234 <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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235 <option value="pp.select_features">Perform feature selection, using 'pp.select_features'</option>
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236 <option value="pp.scrublet">Compute probability of being a doublet using the scrublet algorithm, using 'pp.scrublet'</option>
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237 <option value="pp.filter_doublets">Remove doublets according to the doublet probability or doublet score, using 'pp.filter_doublets'</option>
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238 <option value="pp.mnc_correct">A modified MNN-Correct algorithm based on cluster centroid, using 'pp.mnc_correct'</option>
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239 <option value="pp.harmony">Use harmonypy to integrate different experiments,using 'pp.harmony'</option>
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240 <option value="pp.scanorama_integrate">Use Scanorama [Hie19] to integrate different experiments, using 'pp.scanorama_integrate'</option>
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241 <option value="metrics.frag_size_distr">Compute the fragment size distribution of the dataset, using 'metrics.frag_size_distr'</option>
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242 <option value="metrics.tsse">Compute the TSS enrichment score (TSSe) for each cell, using 'metrics.tsse'</option>
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243 </param>
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244 <when value="pp.make_fragment_file">
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245 <param argument="bam_file" type="data" format="bam" label="File name of the BAM file"/>
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246 <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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247 <conditional name="barcode">
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248 <param name="extract_type" type="select" label="How to extract barcodes from BAM records?">
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249 <option value="from_tag">From TAG fileds</option>
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250 <option value="from_read_names">From read names using regular expressions</option>
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251 </param>
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252 <when value="from_tag">
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253 <param argument="barcode_tag" type="text" value="CB" optional="true" label="Extract barcodes from TAG fields of BAM records"/>
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254 </when>
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255 <when value="from_read_names">
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256 <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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257 </when>
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258 </conditional>
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259 <param argument="umi_tag" type="text" value="" optional="true" label="Extract UMI from TAG fields of BAM records"/>
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260 <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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261 <expand macro="param_shift"/>
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262 <param argument="min_mapq" type="integer" min="0" value="30" label="Filter the reads based on MAPQ"/>
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263 <expand macro="param_chunk_size" size="50000000"/>
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264 </when>
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265 <when value="pp.import_data">
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266 <param argument="fragment_file" type="data" format="interval" label="Fragment file, optionally compressed with gzip or zstd"/>
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267 <param argument="chrom_sizes" type="data" format="tabular" label="A tabular file containing chromosome names and sizes"/>
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268 <param argument="min_num_fragments" type="integer" value="200" label="Number of unique fragments threshold used to filter cells"/>
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269 <param argument="sorted_by_barcode" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether the fragment file has been sorted by cell barcodes"/>
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270 <param argument="whitelist" type="data" format="txt" optional="True" label="Whitelist file with a list of barcodes" help="Each line must contain a valid barcode. When provided, only barcodes in the whitelist will be retained."/>
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271 <param argument="chrM" type="text" value="chrM, M" label="A list of chromosome names that are considered mitochondrial DNA">
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272 <expand macro="sanitize_query"/>
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273 </param>
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274 <param argument="shift_left" type="integer" value="0" label="Insertion site correction for the left end" help="Note this has no effect on single-end reads"/>
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275 <param argument="shift_right" type="integer" value="0" label="Insertion site correction for the right end" help="Note this has no effect on single-end reads"/>
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276 <expand macro="param_chunk_size" size="2000"/>
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277 </when>
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278 <when value="pp.add_tile_matrix">
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279 <expand macro="inputs_anndata"/>
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280 <param argument="bin_size" type="integer" value="500" label="The size of consecutive genomic regions used to record the counts"/>
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281 <expand macro="param_chunk_size" size="500"/>
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282 <param argument="exclude_chroms" type="text" value="chrM, chrY, M, Y" optional="true" label="A list of chromosomes to exclude">
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283 <expand macro="sanitize_query"/>
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284 </param>
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285 <expand macro="min_max_frag_size"/>
1
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286 <expand macro="param_counting_strategy"/>
0
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287 </when>
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288 <when value="pp.make_gene_matrix">
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289 <expand macro="inputs_anndata"/>
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290 <param argument="gene_anno" type="data" format="gtf,gff3" label="GTF/GFF file containing the gene annotation"/>
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291 <expand macro="param_chunk_size" size="500"/>
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292 <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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293 <param argument="id_type" type="select" label="Id type, 'gene' or 'transcript'">
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294 <option value="gene" selected="true">gene</option>
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295 <option value="transcript">transcript</option>
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296 </param>
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297 <param argument="transcript_name_key" type="text" value="transcript_name" label="The key of the transcript name in the gene annotation file"/>
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298 <param argument="transcript_id_key" type="text" value="transcript_id" label="The key of the transcript id in the gene annotation file"/>
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299 <param argument="gene_name_key" type="text" value="gene_name" label="The key of the gene name in the gene annotation file"/>
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300 <param argument="gene_id_key" type="text" value="gene_id" label="The key of the gene id in the gene annotation file"/>
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301 <expand macro="min_max_frag_size"/>
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302 <expand macro="param_counting_strategy"/>
0
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303 </when>
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304 <when value="pp.filter_cells">
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305 <expand macro="inputs_anndata"/>
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306 <param argument="min_counts" type="integer" value="1000" label="Minimum number of counts required for a cell to pass filtering"/>
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307 <param argument="min_tsse" type="float" value="5.0" label="Minimum TSS enrichemnt score required for a cell to pass filtering"/>
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308 <param argument="max_counts" type="integer" value="" optional="true" label="Maximum number of counts required for a cell to pass filtering"/>
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309 <param argument="max_tsse" type="float" value="" optional="true" label="Maximum TSS enrichment score expressed required for a cell to pass filtering"/>
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310 </when>
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311 <when value="pp.select_features">
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312 <expand macro="inputs_anndata"/>
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313 <param argument="n_features" type="integer" min="1" value="500000" label="Number of features to keep"/>
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314 <param argument="filter_lower_quantile" type="float" min="0" value="0.005" label="Lower quantile of the feature count distribution to filter out"/>
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315 <param argument="filter_upper_quantile" type="float" min="0" value="0.005" label="Upper quantile of the feature count distribution to filter out"/>
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316 <param argument="whitelist" type="data" format="bed" optional="true" label="A user provided bed file containing genome-wide whitelist regions"/>
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317 <param argument="blacklist" type="data" format="bed" optional="true" label="A user provided bed file containing genome-wide blacklist regions"/>
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318 <param argument="max_iter" type="integer" value="1" label="If greater than 1, this function will perform iterative clustering and feature selection"/>
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319 </when>
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320 <when value="pp.scrublet">
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321 <expand macro="inputs_anndata"/>
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322 <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."/>
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323 <param argument="n_comps" type="integer" value="15" label="Number of components" help="15 is usually sufficient. The algorithm is not sensitive to this parameter"/>
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324 <param argument="sim_doublet_ratio" type="float" value="2.0" label="Number of doublets to simulate relative to the number of observed cells"/>
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325 <param argument="expected_doublet_rate" type="float" value="0.1" label="Expected doublet rate"/>
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326 <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"/>
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327 <param argument="use_approx_neighbors" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Whether to use approximate search"/>
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328 <param argument="random_state" type="integer" value="0" label="Random state"/>
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329 </when>
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330 <when value="pp.filter_doublets">
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331 <expand macro="inputs_anndata"/>
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332 <param argument="probability_threshold" type="float" value="0.5" label="Threshold for doublet probability"/>
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333 <param argument="score_threshold" type="float" value="" optional="true" label="Threshold for doublet score"/>
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334 </when>
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335 <when value="pp.mnc_correct">
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336 <expand macro="inputs_anndata"/>
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337 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
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338 <expand macro="sanitize_query"/>
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339 </param>
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340 <param argument="n_neighbors" type="integer" value="5" label="Number of mutual nearest neighbors"/>
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341 <param argument="n_clusters" type="integer" value="40" label="Number of clusters"/>
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342 <param argument="n_iter" type="integer" value="1" label="Number of iterations"/>
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343 <expand macro="params_data_integration"/>
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344 </when>
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345 <when value="pp.harmony">
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346 <expand macro="inputs_anndata"/>
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347 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
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348 <expand macro="sanitize_query"/>
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349 </param>
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350 <expand macro="params_data_integration"/>
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351 </when>
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352 <when value="pp.scanorama_integrate">
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353 <expand macro="inputs_anndata"/>
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354 <param argument="batch" type="text" value="batch" label="Batch labels for cells">
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355 <expand macro="sanitize_query"/>
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356 </param>
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357 <param argument="n_neighbors" type="integer" value="20" label="Number of mutual nearest neighbors"/>
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358 <expand macro="params_data_integration"/>
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359 </when>
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360 <when value="metrics.frag_size_distr">
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361 <!-- TODO move this to plotting -->
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362 <expand macro="inputs_anndata"/>
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363 <param argument="max_recorded_size" type="integer" min="1" value="1000" label="The maximum fragment size to record in the result"/>
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364 <param argument="add_key" type="text" value="frag_size_distr" label="Key used to store the result in `adata.uns`"/>
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365 </when>
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366 <when value="metrics.tsse">
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diff changeset
367 <!-- TODO move this to plotting -->
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368 <expand macro="inputs_anndata"/>
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369 <param argument="gene_anno" type="data" format="gtf,gff3" label="GTF/GFF file containing the gene annotation"/>
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370 </when>
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371 </conditional>
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372 <expand macro="inputs_common_advanced"/>
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373 </inputs>
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diff changeset
374 <outputs>
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375 <data name="fragments_out" format="interval" label="${tool.name} (${method.method}) on ${on_string}: Fragment file">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
376 <filter>method['method'] == 'pp.make_fragment_file'</filter>
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diff changeset
377 </data>
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378 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
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diff changeset
379 <filter>method['method'] != 'pp.make_fragment_file'</filter>
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diff changeset
380 </data>
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381 <data name="hidden_output" format="txt" label="Log file">
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diff changeset
382 <filter>advanced_common['show_log']</filter>
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383 </data>
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diff changeset
384 </outputs>
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diff changeset
385 <tests>
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386 <test expect_num_outputs="1">
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387 <!-- pp.make_fragment_file -->
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diff changeset
388 <conditional name="method">
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389 <param name="method" value="pp.make_fragment_file"/>
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diff changeset
390 <param name="bam_file" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21_subsample.bam"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
391 <param name="is_paired" value="true"/>
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diff changeset
392 <conditional name="barcode">
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393 <param name="extract_type" value="from_tag"/>
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394 <param name="barcode_tag" value="CB"/>
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395 </conditional>
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diff changeset
396 <param name="shift_left" value="4"/>
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397 <param name="shift_right" value="-5"/>
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398 <param name="min_mapq" value="10"/>
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399 <param name="chunk_size" value="50000000"/>
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400 </conditional>
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diff changeset
401 <output name="fragments_out" location="https://zenodo.org/records/11260316/files/pp.make_fragment_file.pbmc_500_chr21.tsv.gz" ftype="interval" compare="sim_size" delta_frac="0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
402 </test>
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403 <test expect_num_outputs="2">
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diff changeset
404 <!-- pp.pp.import_data -->
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parents:
diff changeset
405 <conditional name="method">
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406 <param name="method" value="pp.import_data"/>
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diff changeset
407 <param name="fragment_file" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21.tsv.gz"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
408 <param name="chrom_sizes" location="https://zenodo.org/records/11260316/files/chr21_size.tabular"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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409 <param name="min_num_fragments" value="1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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parents:
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410 <param name="sorted_by_barcode" value="False"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
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diff changeset
411 <param name="shift_left" value="0"/>
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parents:
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412 <param name="chrM" value="chrM, M"/>
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parents:
diff changeset
413 <param name="shift_right" value="0"/>
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414 <param name="chunk_size" value="1000"/>
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415 </conditional>
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diff changeset
416 <section name="advanced_common">
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417 <param name="show_log" value="true"/>
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418 </section>
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diff changeset
419 <output name="hidden_output">
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iuc
parents:
diff changeset
420 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
421 <has_text_matching expression="sa.pp.import_data"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
422 <has_text_matching expression="min_num_fragments = 1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
423 <has_text_matching expression="sorted_by_barcode = False"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
424 <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
425 <has_text_matching expression="chrM = \['chrM', 'M'\]"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
426 <has_text_matching expression="shift_right = 0"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
427 <has_text_matching expression="chunk_size = 1000"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
428 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
429 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
430 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
431 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
432 <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
433 <!-- 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
434 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
435 <param name="method" value="pp.make_gene_matrix"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
436 <param name="adata" location="https://zenodo.org/records/11260316/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
437 <param name="gene_anno" location="https://zenodo.org/records/11260316/files/chr21.gff3.gz"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
438 <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
439 <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
440 <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
441 <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
442 <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
443 <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
444 <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
445 <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
446 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
447 <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
448 <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
449 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
450 <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
451 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
452 <has_text_matching expression="sa.pp.make_gene_matrix"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
453 <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
454 <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
455 <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
456 <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
457 <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
458 <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
459 <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
460 <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
461 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
462 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
463 <output name="anndata_out" location="https://zenodo.org/records/12548681/files/pp.make_gene_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
464 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
465 <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
466 <!-- metrics.tsse -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
467 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
468 <param name="method" value="metrics.tsse"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
469 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
470 <param name="gene_anno" location="https://zenodo.org/records/11260316/files/chr21.gff3.gz"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
471 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
472 <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
473 <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
474 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
475 <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
476 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
477 <has_text_matching expression="sa.metrics.tsse"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
478 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
479 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
480 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
481 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
482 <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
483 <!-- pp.filter_cells -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
484 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
485 <param name="method" value="pp.filter_cells"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
486 <param name="adata" location="https://zenodo.org/records/11260316/files/metrics.tsse.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
487 <param name="min_counts" value="200"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
488 <param name="min_tsse" value="5"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
489 <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
490 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
491 <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
492 <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
493 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
494 <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
495 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
496 <has_text_matching expression="sa.pp.filter_cells"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
497 <has_text_matching expression="min_counts = 200"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
498 <has_text_matching expression="min_tsse = 5"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
499 <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
500 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
501 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
502 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
503 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
504 <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
505 <!-- 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
506 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
507 <param name="method" value="pp.add_tile_matrix"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
508 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
509 <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
510 <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
511 <param name="exclude_chroms" value="chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr22, chrX, chrY"/>
1
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
512 <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
513 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
514 <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
515 <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
516 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
517 <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
518 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
519 <has_text_matching expression="sa.pp.add_tile_matrix"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
520 <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
521 <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
522 <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
1
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
523 <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
524 </assert_contents>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
525 </output>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
526 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
527 </test>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
528 <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
529 <!-- 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
530 <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
531 <param name="method" value="pp.add_tile_matrix"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
532 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.filter_cells.pbmc_500_chr21.h5ad"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
533 <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
534 <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
535 <param name="exclude_chroms" value="chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr22, chrX, chrY"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
536 <param name="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
537 </conditional>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
538 <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
539 <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
540 </section>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
541 <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
542 <assert_contents>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
543 <has_text_matching expression="sa.pp.add_tile_matrix"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
544 <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
545 <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
546 <has_text_matching expression="exclude_chroms = \['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr22', 'chrX', 'chrY'\]"/>
e3b85e48487b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
iuc
parents: 0
diff changeset
547 <has_text_matching expression="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
548 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
549 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
550 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
551 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
552 <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
553 <!-- pp.select_features -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
554 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
555 <param name="method" value="pp.select_features"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
556 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.add_tile_matrix.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
557 <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
558 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
559 <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
560 <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
561 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
562 <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
563 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
564 <has_text_matching expression="sa.pp.select_features"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
565 <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
566 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
567 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
568 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.select_features.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
569 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
570 <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
571 <!-- pp.scrublet -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
572 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
573 <param name="method" value="pp.scrublet"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
574 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.select_features.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
575 <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
576 <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
577 <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
578 <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
579 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
580 <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
581 <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
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>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
585 <has_text_matching expression="sa.pp.scrublet"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
586 <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
587 <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
588 <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
589 <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
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>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
592 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.scrublet.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
593 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
594 <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
595 <!-- pp.filter_doublets -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
596 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
597 <param name="method" value="pp.filter_doublets"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
598 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.scrublet.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
599 <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
600 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
601 <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
602 <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
603 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
604 <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
605 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
606 <has_text_matching expression="sa.pp.filter_doublets"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
607 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
608 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
609 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.filter_doublets.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
610 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
611 <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
612 <!-- pp.mnc_correct -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
613 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
614 <param name="method" value="pp.mnc_correct"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
615 <param name="adata" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21.batch.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
616 <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
617 <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
618 <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
619 <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
620 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
621 <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
622 <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
623 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
624 <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
625 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
626 <has_text_matching expression="sa.pp.mnc_correct"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
627 <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
628 <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
629 <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
630 <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
631 <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
632 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
633 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
634 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.mnc_correct.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
635 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
636 <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
637 <!-- pp.harmony -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
638 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
639 <param name="method" value="pp.harmony"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
640 <param name="adata" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21.batch.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
641 <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
642 <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
643 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
644 <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
645 <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
646 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
647 <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
648 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
649 <has_text_matching expression="sa.pp.harmony"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
650 <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
651 <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
652 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
653 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
654 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.harmony.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
655 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
656 <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
657 <!-- pp.scanorama_integrate -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
658 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
659 <param name="method" value="pp.scanorama_integrate"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
660 <param name="adata" location="https://zenodo.org/records/11260316/files/pbmc_500_chr21.batch.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
661 <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
662 <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
663 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
664 <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
665 <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
666 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
667 <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
668 <assert_contents>
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="sa.pp.scanorama_integrate"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
670 <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
671 <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
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>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
674 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.scanorama_integrate.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
675 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
676 <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
677 <!-- metrics.frag_size_distr -->
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
678 <conditional name="method">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
679 <param name="method" value="metrics.frag_size_distr"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
680 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.import_data.pbmc_500_chr21.h5ad"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
681 <param name="max_recorded_size" value="500"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
682 <param name="add_key" value="frag_size_distr"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
683 </conditional>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
684 <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
685 <param name="show_log" value="true" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
686 </section>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
687 <output name="hidden_output">
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
688 <assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
689 <has_text_matching expression="sa.metrics.frag_size_distr"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
690 <has_text_matching expression="add_key = 'frag_size_distr'"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
691 </assert_contents>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
692 </output>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
693 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/metrics.frag_size_distr.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
694 </test>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
695 </tests>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
696 <help><![CDATA[
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
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diff changeset
697 Convert a BAM file`to a fragment file, using `pp.make_fragment_file`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
698 ====================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
699
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
700 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
701
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
702 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
703
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
704 - 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
705
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
706 - 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
707
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
708 - 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
709
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
710 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
711
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
712 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
713 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.make_fragment_file.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
714
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
715 Import data fragment file` and compute basic QC metrics, using `pp.import_data`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
716 ===============================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
717
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
718 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
719
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
720 A fragment refers to the sequence data originating from a distinct location in the genome. In single-ended sequencing, one read equates to a fragment. However, in paired-ended sequencing, a fragment is defined by a pair of reads. This function is designed to handle, store, and process input files with fragment data, further yielding a range of basic Quality Control (QC) metrics. These metrics include the total number of unique fragments, duplication rates, and the percentage of mitochondrial DNA detected.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
721
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
722 How fragments are stored is dependent on the sequencing approach utilized. For single-ended sequencing, fragments are found in `.obsm['fragment_single']`. In contrast, for paired-ended sequencing, they are located in `.obsm['fragment_paired']`.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
723
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
724 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
725 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.import_data.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
726
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
727 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
728 =============================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
729
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
730 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
731
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
732 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
733
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
734 `import_data` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
735
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
736 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
737 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.add_tile_matrix.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
738
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
739 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
740 ==================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
741
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
742 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
743
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
744 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
745
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
746 `import_data` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
747
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
748 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
749 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.make_gene_matrix.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
750
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
751 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
752 ============================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
753
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
754 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
755
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
756 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
757 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.filter_cells.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
758
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
759 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
760 =====================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
761
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
762 Perform feature selection by selecting the most accessibile features across all cells unless `max_iter` > 1
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
763
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
764 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
765 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.select_features.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
766
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
767 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
768 ========================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
769
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
770 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
771
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
772 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
773
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
774 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
775 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.scrublet.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
776
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
777 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
778 =================================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
779
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
780 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
781
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
782 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
783
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
784 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
785 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.filter_doublets.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
786
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
787 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
788 ==================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
789
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
790 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
791
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
792 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
793 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.mnc_correct.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
794
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
795 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
796 ===================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
797
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
798 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
799
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
800 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
801
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
802 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
803 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.harmony.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
804
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
805 Use Scanorama to integrate different experiments, using `pp.scanorama_integrate`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
806 ========================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
807
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
808 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
809
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
810 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
811
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
812 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
813 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.scanorama_integrate.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
814
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
815 Compute the fragment size distribution of the dataset, using `metrics.frag_size_distr`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
816 ======================================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
817
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
818 Compute the fragment size distribution of the dataset.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
819
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
820 This function computes the fragment size distribution of the dataset. Note that it does not operate at the single-cell level. The result is stored in a vector where each element represents the number of fragments and the index represents the fragment length. The first posision of the vector is reserved for fragments with size larger than the `max_recorded_size` parameter. `import_data` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
821
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
822 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
823 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.metrics.frag_size_distr.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
824
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
825 Compute the TSS enrichment score (TSSe) for each cell, using `metrics.tsse`
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
826 ===========================================================================
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
827
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
828 Compute the TSS enrichment score (TSSe) for each cell.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
829
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
830 `import_data` must be ran first in order to use this function.
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
831
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
832 More details on the `SnapATAC2 documentation
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
833 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.metrics.tsse.html>`__
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
834
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
835 ]]></help>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
836 <expand macro="citations"/>
b2844c6efb72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit df9c285dddde7d901823c608c8d7dab971224b5b
iuc
parents:
diff changeset
837 </tool>