Mercurial > repos > iuc > peaks_and_motif

annotate peaks_and_motif_analysis.xml @ 0:1c52ce622590 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
author iuc
date Thu, 23 May 2024 15:19:50 +0000
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1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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1 <tool id="peaks_and_motif" name="SnapATAC2 peaks and motif" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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2 <description>analysis</description>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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3 <macros>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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4 <import>macros.xml</import>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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5 </macros>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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6 <requirements>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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7 <expand macro="requirements"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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8 </requirements>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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9 <command detect_errors="exit_code"><![CDATA[
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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10 export NUMBA_CACHE_DIR="\${TEMP:-/tmp}";
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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11 @PREP_ADATA@
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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12 @CMD@
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13 ]]></command>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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14 <configfiles>
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15 <configfile name="script_file"><![CDATA[
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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16 @CMD_imports@
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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17 @CMD_read_inputs@
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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18
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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19 #if $method.method == 'tl.macs3'
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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20 if __name__ == '__main__': ## a temporary fix https://github.com/kaizhang/SnapATAC2/issues/298
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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21 sa.tl.macs3(
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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22 adata,
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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23 #if $method.groupby != ''
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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24 groupby = '$method.groupby',
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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25 #end if
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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26 qvalue = $method.qvalue,
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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27 #if $method.replicate
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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28 replicate = '$method.replicate',
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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29 #end if
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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30 #if $method.replicate_qvalue
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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31 replicate_qvalue = $method.replicate_qvalue,
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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32 #end if
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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33 #if $method.max_frag_size
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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34 max_frag_size = $method.max_frag_size,
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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35 #end if
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36 nolambda = $method.nolambda,
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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37 shift = $method.shift,
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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38 extsize = $method.extsize,
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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39 #if $method.blacklist
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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40 blacklist = '$method.blacklist',
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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41 #end if
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42 key_added = '$method.key_added',
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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43 inplace = True,
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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44 tempdir = '.',
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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45 n_jobs = 1
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46 )
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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47
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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48 #else if $method.method == 'tl.merge_peaks'
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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49 import json
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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50 import pandas as pd
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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51 import csv
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52 with open('$method.chrom_sizes') as f:
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53 chr_sizes = {x[0]:int(x[1]) for x in csv.reader(f, delimiter='\t')}
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54
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55 peaks = sa.tl.merge_peaks(
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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56 adata.uns['$method.macs_key'],
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57 chrom_sizes = chr_sizes,
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58 half_width = $method.half_width
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59 )
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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60 peaks.write_csv('merged_peaks.tabular', separator = '\t')
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61
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62 #else if $method.method == 'pp.make_peak_matrix'
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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63 import polars
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64 peaks = polars.read_csv('$method.merged_peaks', separator='\t')
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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65 sa.pp.make_peak_matrix(
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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66 adata,
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67 use_rep = peaks['Peaks'],
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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68 chunk_size = $method.chunk_size,
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69 use_x = $method.use_x,
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70 #if $method.min_frag_size
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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71 min_frag_size = $method.min_frag_size,
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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72 #end if
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73 #if $method.max_frag_size
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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74 max_frag_size = $method.max_frag_size,
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75 #end if
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76 ##counting_strategy = '$method.counting_strategy'
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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77 count_frag_as_reads = $method.count_frag_as_reads
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78 )
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79
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80 #else if $method.method == 'tl.marker_regions'
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81 marker_peaks = sa.tl.marker_regions(
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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82 adata,
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83 groupby = '$method.groupby',
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84 pvalue = $method.pvalue
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85 )
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86 sa.pl.regions(
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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87 adata,
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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88 groupby = '$method.groupby',
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89 peaks = marker_peaks,
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90 @CMD_params_render_plot@
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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91 )
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92
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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93
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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94 #else if $method.method == 'tl.diff_test'
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95 import numpy as np
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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96 import polars
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97 peaks = polars.read_csv('$method.merged_peaks', separator='\t')
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98 group_key = '$method.group_key'
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99 #if $method.compare.with == 'single_group'
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100 group1 = '$method.compare.group1_value'
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101 group1_cells = adata.obs[group_key] == group1
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102 group2 = '$method.compare.group2_value'
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103 group2_cells = adata.obs[group_key] == group2
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104 peaks_selected = np.logical_or(
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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105 peaks[group1].to_numpy(),
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106 peaks[group2].to_numpy(),
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107 )
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108 #else if $method.compare.with == 'background_group'
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109 group1 = '$method.compare.group1_value'
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110 group1_cells = adata.obs[group_key] == group1
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111 barcodes = np.array(adata.obs_names)
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112 group2_cells = []
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113 for i in np.unique(adata.obs[group_key]):
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114 if i != group1:
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115 cells = np.random.choice(barcodes[adata.obs[group_key] == i], size=$method.compare.number_of_cells, replace=False)
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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116 group2_cells.append(cells)
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117 group2_cells = np.concatenate(group2_cells)
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118 peaks_selected = peaks[group1].to_numpy()
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119 #end if
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120
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121 diff_peaks = sa.tl.diff_test(
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122 adata,
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123 cell_group1 = group1_cells,
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124 cell_group2 = group2_cells,
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125 features = peaks_selected,
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126 direction = '$method.direction',
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127 min_log_fc = $method.min_log_fc,
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128 min_pct = $method.min_pct
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129 )
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130 diff_peaks.write_csv('diff_peaks.tabular', separator = '\t')
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131
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132 diff_peaks = diff_peaks.filter(polars.col('adjusted p-value') < $method.cutoff_p_adj)
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133
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134 #if $method.compare.with == 'single_group'
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135 peaks_to_plot = {
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136 group1: diff_peaks.filter(polars.col("log2(fold_change)") > $method.cutoff_l2fc)['feature name'].to_numpy(),
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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137 group2: diff_peaks.filter(polars.col("log2(fold_change)") < $method.cutoff_l2fc)['feature name'].to_numpy(),
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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138 }
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139 #else if $method.compare.with == 'background_group'
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140 peaks_to_plot = {
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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141 group1: diff_peaks['feature name'].to_numpy()
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142 }
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143 #end if
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144
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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145 sa.pl.regions(
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146 adata,
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147 groupby = group_key,
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148 peaks = peaks_to_plot,
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149 @CMD_params_render_plot@
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150 )
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151
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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152 #end if
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153 @CMD_anndata_write_outputs@
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154 ]]></configfile>
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155 </configfiles>
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156 <inputs>
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157 <conditional name="method">
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158 <param name="method" type="select" label="Tool">
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159 <option value="tl.macs3">Call peaks using MACS3, using 'tl.macs3'</option>
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160 <option value="tl.merge_peaks">Merge peaks from different groups, using 'tl.merge_peaks'</option>
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161 <option value="pp.make_peak_matrix">Generate cell by peak count matrix, using 'pp.make_peak_matrix'</option>
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162 <option value="tl.marker_regions">A quick-and-dirty way to get marker regions, using 'tl.marker_regions'</option>
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163 <option value="tl.diff_test">Identify differentially accessible regions,using 'tl.diff_test'</option>
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164 </param>
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165 <when value="tl.macs3">
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166 <expand macro="inputs_anndata"/>
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167 <param argument="groupby" type="text" value="" optional="true" label="Group cells before peak calling based on key in `.obs`"/>
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168 <param argument="qvalue" type="float" value="0.05" label="qvalue cutoff used in MACS3"/>
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169 <param argument="replicate" type="text" value="" optional="true" label="Replicate information based on key in `.obs`"/>
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170 <param argument="replicate_qvalue" type="float" value="" optional="true" label="qvalue cutoff used in MACS3 for calling peaks in replicates"/>
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171 <param argument="max_frag_size" type="integer" value="" optional="true" label="Maximum fragment size"
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172 help="This is used to remove fragments that are not from nucleosome-free regions."/>
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173 <param argument="nolambda" type="boolean" checked="false" truevalue="True" falsevalue="False" label="If True, macs3 will use the background lambda as local lambda"/>
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174 <param argument="shift" type="integer" value="-100" label="The shift size in MACS"/>
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175 <param argument="extsize" type="integer" value="200" label="The extension size in MACS"/>
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176 <param argument="blacklist" type="data" format="bed" optional="true" label="Blacklist file in BED format"
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177 help="If provided, regions in the blacklist will be removed."/>
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178 <param argument="key_added" type="text" value="macs3" label="`.uns` key under which to add peak information"/>
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179 </when>
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180 <when value="tl.merge_peaks">
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181 <expand macro="inputs_anndata"/>
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182 <param name="macs_key" type="text" value="macs3" label="`.uns` key under which peak information was added while peak calling"/>
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183 <param argument="chrom_sizes" type="data" format="tabular" label="Chromosome sizes"/>
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184 <param argument="half_width" type="integer" value="250" label="Half width of the merged peaks"/>
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185 </when>
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186 <when value="pp.make_peak_matrix">
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187 <expand macro="inputs_anndata"/>
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188 <param argument="use_rep" type="text" optional="true" value="" label="Used to read peak information from .uns[use_rep]">
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189 <expand macro="sanitize_query"/>
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190 </param>
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191 <param argument="merged_peaks" type="data" format="tabular" label="Merged peaks file"/>
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192 <expand macro="param_chunk_size" size="500"/>
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193 <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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194 <expand macro="min_max_frag_size"/>
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195 <!--expand macro="param_counting_strategy"/-->
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196 <param argument="count_frag_as_reads" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to count fragments as reads"/>
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197 </when>
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198 <when value="tl.marker_regions">
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199 <expand macro="inputs_anndata"/>
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200 <expand macro="param_groupby"/>
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201 <param argument="pvalue" type="float" value="0.01" label="P-value threshold"/>
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202 <expand macro="params_render_plot"/>
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203 </when>
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204 <when value="tl.diff_test">
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205 <expand macro="inputs_anndata"/>
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206 <param argument="merged_peaks" type="data" format="tabular" label="Merged peaks file"/>
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207 <param name="group_key" type="text" value="cell_type" label="key in `.obs` to select cell groups" help="for eg. cell_type"/>
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208 <conditional name="compare">
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209 <param name="with" type="select" label="Test for differential accessibility in a group of cells compared to">
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210 <option value="single_group">Another group of cells</option>
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211 <option value="background_group">Background cell group built from random selection of cells from all other the groups</option>
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212 </param>
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213 <when value="single_group">
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214 <param name="group1_value" type="text" value="Naive B" label="name of the group 1 stored in .obs"/>
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215 <param name="group2_value" type="text" value="Memory B" label="name of the group 2 stored in .obs"/>
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216 </when>
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217 <when value="background_group">
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218 <param name="group1_value" type="text" value="Naive B" label="name of the group 1 stored in .obs"/>
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219 <param name="number_of_cells" type="integer" min="1" value="30" label="Number of cells to subsample from ther other groups"/>
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220 </when>
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221 </conditional>
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222 <param argument="direction" type="select" label="“positive”: return features that are enriched in group 1. “negative”: return features that are enriched in group 2">
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223 <option value="positive">“positive”: return features that are enriched in group 1</option>
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224 <option value="negative"> “negative”: return features that are enriched in group 2</option>
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225 <option value="both" selected="true">“both”: return features that are enriched in group 1 or group 2</option>
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226 </param>
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227 <param argument="min_log_fc" type="float" value="0.25" label="Limit testing to features which show, on average, at least this difference (log2-scale) between the two groups of cells"/>
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228 <param argument="min_pct" type="float" value="0.05" label="Only test features that are detected in a minimum fraction of min_pct cells in either of the two population"/>
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229 <expand macro="params_render_plot"/>
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230 <param name="cutoff_p_adj" type="float" value="0.01" label="Adjusted p-value cutoff for plotting" help="This cutoff is applied for plotting only"/>
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231 <param name="cutoff_l2fc" type="float" value="1" label="Log2 fold change cutoff for plotting" help="This cutoff is applied for plotting only"/>
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232 </when>
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233 </conditional>
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234 <expand macro="inputs_common_advanced"/>
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235 </inputs>
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236 <outputs>
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237 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
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238 <data name="hidden_output" format="txt" label="Log file" >
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239 <filter>advanced_common['show_log']</filter>
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240 </data>
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241 <data name="merged_peaks" format="tabular" from_work_dir="merged_peaks.tabular" label="${tool.name} (${method.method}) on ${on_string}: Merged peaks">
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242 <filter>method['method'] == 'tl.merge_peaks'</filter>
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243 </data>
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244 <data name="out_png" format="png" from_work_dir="plot.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
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245 <filter>(method['method'] == 'tl.marker_regions' or method['method'] == 'tl.diff_test') and method['out_file'] == 'png'</filter>
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246 </data>
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247 <data name="out_pdf" format="pdf" from_work_dir="plot.pdf" label="PDF plot from ${tool.name} (${method.method}) on ${on_string}">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
248 <filter>(method['method'] == 'tl.marker_regions' or method['method'] == 'tl.diff_test') and method['out_file'] == 'pdf'</filter>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
249 </data>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
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250 <data name="out_svg" format="svg" from_work_dir="plot.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
251 <filter>(method['method'] == 'tl.marker_regions' or method['method'] == 'tl.diff_test') and method['out_file'] == 'svg'</filter>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
252 </data>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
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253 <data name="diff_peaks" format="tabular" from_work_dir="diff_peaks.tabular" label="${tool.name} on ${on_string}: Differential peaks" >
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
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254 <filter>method['method'] == 'tl.diff_test'</filter>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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255 </data>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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256 </outputs>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
257 <tests>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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258 <test expect_num_outputs="2">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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259 <!-- tl.macs3 -->
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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260 <conditional name="method">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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261 <param name="method" value="tl.macs3"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
262 <param name="adata" location="https://zenodo.org/records/11260316/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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263 <param name="groupby" value="leiden"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
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264 <param name="qvalue" value="0.1"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
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265 <param name="shift" value="-100"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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266 <param name="extsize" value="200"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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267 <param name="key_added" value="macs3"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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268 </conditional>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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269 <section name="advanced_common">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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270 <param name="show_log" value="true"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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271 </section>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
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272 <output name="hidden_output">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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273 <assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
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274 <has_text_matching expression="sa.tl.macs3"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
275 <has_text_matching expression="groupby = 'leiden'"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
276 <has_text_matching expression="qvalue = 0.1"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
277 <has_text_matching expression="shift = -100"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
278 <has_text_matching expression="extsize = 200"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
279 <has_text_matching expression="key_added = 'macs3'"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
280 </assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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281 </output>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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282 <output name="anndata_out" ftype="h5ad" compare="sim_size" delta="20000" location="https://zenodo.org/records/11260316/files/tl.macs3.pbmc_500_chr21.h5ad"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
283 </test>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
284 <test expect_num_outputs="3">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
285 <!-- tl.merge_peaks -->
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
286 <conditional name="method">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
287 <param name="method" value="tl.merge_peaks"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
288 <param name="adata" location="https://zenodo.org/records/11260316/files/tl.macs3.pbmc_500_chr21.h5ad"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
289 <param name="chrom_sizes" location="https://zenodo.org/records/11260316/files/chr21_size.tabular"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
290 <param name="half_width" value="250"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
291 </conditional>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
292 <section name="advanced_common">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
293 <param name="show_log" value="true" />
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
294 </section>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
295 <output name="hidden_output">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
296 <assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
297 <has_text_matching expression="sa.tl.merge_peaks"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
298 <has_text_matching expression="half_width = 250"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
299 </assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
300 </output>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
301 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/tl.merge_peaks.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
302 <output name="merged_peaks" >
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
303 <assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
304 <has_text_matching expression="chr21:5063027-5063528"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
305 <has_text_matching expression="chr21:19782380-19782881"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
306 <has_text_matching expression="chr21:29908867-29909368"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
307 <has_text_matching expression="chr21:37392823-37393324"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
308 <has_text_matching expression="chr21:44082467-44082968"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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diff changeset
309 </assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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diff changeset
310 </output>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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diff changeset
311 </test>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
312 <test expect_num_outputs="2">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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diff changeset
313 <!-- pp.make_peak_matrix -->
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
314 <conditional name="method">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
315 <param name="method" value="pp.make_peak_matrix"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
316 <param name="adata" location="https://zenodo.org/records/11260316/files/tl.merge_peaks.pbmc_500_chr21.h5ad"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
317 <param name="merged_peaks" location="https://zenodo.org/records/11260316/files/merged_peaks.tabular"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
318 <param name="chunk_size" value="500"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
319 <param name="use_x" value="False"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
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320 <param name="count_frag_as_reads" value="True"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
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321 </conditional>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
322 <section name="advanced_common">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
323 <param name="show_log" value="true" />
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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324 </section>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
325 <output name="hidden_output">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
326 <assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
327 <has_text_matching expression="sa.pp.make_peak_matrix"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
328 <has_text_matching expression="chunk_size = 500"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
329 <has_text_matching expression="use_x = False"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
330 <has_text_matching expression="count_frag_as_reads = True"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
331 </assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
332 </output>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
333 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/pp.make_peak_matrix.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
334 </test>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
335 <test expect_num_outputs="3">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
336 <!-- tl.marker_regions -->
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
337 <conditional name="method">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
338 <param name="method" value="tl.marker_regions"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
339 <param name="adata" location="https://zenodo.org/records/11260316/files/pp.make_peak_matrix.pbmc_500_chr21.h5ad"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
340 <param name="groupby" value="leiden"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
341 <param name="pvalue" value="0.1"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
342 <param name="out_file" value="png"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
343 <expand macro="render_plot_test"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
344 </conditional>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
345 <section name="advanced_common">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
346 <param name="show_log" value="true" />
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
347 </section>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
348 <output name="hidden_output">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
349 <assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
350 <has_text_matching expression="sa.tl.marker_regions"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
351 <has_text_matching expression="sa.pl.regions"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
352 <has_text_matching expression="groupby = 'leiden'"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
353 <has_text_matching expression="pvalue = 0.1"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
354 <expand macro="render_plot_matching_text"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
355 </assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
356 </output>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
357 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/tl.marker_regions.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
358 <output name="out_png" location="https://zenodo.org/records/11260316/files/tl.marker_regions.pbmc_500_chr21.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
359 </test>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
360 <test expect_num_outputs="4">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
361 <!-- tl.diff_test single_group -->
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
362 <conditional name="method">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
363 <param name="method" value="tl.diff_test"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
364 <param name="adata" location="https://zenodo.org/records/11260316/files/tl.marker_regions.pbmc_500_chr21.h5ad"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
365 <param name="merged_peaks" location="https://zenodo.org/records/11260316/files/merged_peaks.tabular"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
366 <param name="group_key" value="leiden"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
367 <conditional name="compare">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
368 <param name="with" value="single_group"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
369 <param name="group1_value" value="1"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
370 <param name="group2_value" value="2"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
371 </conditional>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
372 <param name="direction" value="both"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
373 <param name="min_log_fc" value="0.25"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
374 <param name="min_pct" value="0.05"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
375 </conditional>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
376 <section name="advanced_common">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
377 <param name="show_log" value="true" />
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
378 </section>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
379 <output name="hidden_output">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
380 <assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
381 <has_text_matching expression="sa.tl.diff_test"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
382 <has_text_matching expression="group_key = 'leiden'"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
383 <has_text_matching expression="group1 = '1'"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
384 <has_text_matching expression="group2 = '2'"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
385 </assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
386 </output>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
387 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/tl.diff_test.single_group.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
388 <output name="diff_peaks" >
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
389 <assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
390 <has_text_matching expression="chr21:14215000-14220000\t-1.5951.*\t0.0016.*\t0.0563.*"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
391 <has_text_matching expression="chr21:17690000-17695000\t2.2792.*\t0.0996.*\t0.2127.*"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
392 <has_text_matching expression="chr21:13975000-13980000\t0.5423.*\t0.9829.*\t0.9829.*"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
393 </assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
394 </output>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
395 <output name="out_png" location="https://zenodo.org/records/11260316/files/tl.diff_test.single_group.pbmc_500_chr21.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
396 </test>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
397 <test expect_num_outputs="4">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
398 <!-- tl.diff_test background_group -->
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
399 <conditional name="method">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
400 <param name="method" value="tl.diff_test"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
401 <param name="adata" location="https://zenodo.org/records/11260316/files/tl.marker_regions.pbmc_500_chr21.h5ad"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
402 <param name="merged_peaks" location="https://zenodo.org/records/11260316/files/merged_peaks.tabular"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
403 <param name="group_key" value="leiden"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
404 <conditional name="compare">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
405 <param name="with" value="background_group"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
406 <param name="group1_value" value="1"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
407 <param name="number_of_cells" value="2"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
408 </conditional>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
409 <param name="direction" value="positive"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
410 <param name="min_log_fc" value="0.25"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
411 <param name="min_pct" value="0.05"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
412 <param name="cutoff_p_adj" value="0.5"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
413 <param name="cutoff_l2fc" value="0.5"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
414 </conditional>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
415 <section name="advanced_common">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
416 <param name="show_log" value="true" />
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
417 </section>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
418 <output name="hidden_output">
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
419 <assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
420 <has_text_matching expression="sa.tl.diff_test"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
421 <has_text_matching expression="group_key = 'leiden'"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
422 <has_text_matching expression="group1 = '1'"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
423 </assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
424 </output>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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425 <output name="anndata_out" location="https://zenodo.org/records/11260316/files/tl.diff_test.background_group.pbmc_500_chr21.h5ad" ftype="h5ad" compare="sim_size" delta_frac="0.1" />
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
426 <output name="diff_peaks" >
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
427 <assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
428 <has_text_matching expression="chr21:13880000-13885000"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
429 </assert_contents>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
430 </output>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
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431 <output name="out_png" location="https://zenodo.org/records/11260316/files/tl.diff_test.background_group.pbmc_500_chr21.png" ftype="png" compare="sim_size" delta_frac="0.5"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
432 </test>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
433 </tests>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
434 <help><![CDATA[
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
435 Call peaks using MACS3, using `tl.macs3`
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
436 ========================================
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
437
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
438 Call peaks using MACS3.
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
439
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
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diff changeset
440 More details on the `SnapATAC2 documentation
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
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441 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.tl.macs3.html>`__
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
442
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
443 Merge peaks from different groups, using `tl.merge_peaks`
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
444 =========================================================
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
445
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
446 Merge peaks from different groups.
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
447
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
448 Merge peaks from different groups. It is typically used to merge results from `macs3`.
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
449
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
450 This function initially expands the summits of identified peaks by `half_width` on both sides. Following this expansion, it addresses the issue of overlapping peaks through an iterative process. The procedure begins by prioritizing the most significant peak, determined by the smallest p-value. This peak is retained, and any peak that overlaps with it is excluded. Subsequently, the same method is applied to the next most significant peak. This iteration continues until all peaks have been evaluated, resulting in a final list of non-overlapping peaks, each with a fixed width determined by the initial extension.
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
451
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
452 More details on the `SnapATAC2 documentation
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
453 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.tl.merge_peaks.html>`__
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
454
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
455 Generate cell by bin count matrix, using `pp.add_tile_matrix`
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
456 =============================================================
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
457
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
458 Generate cell by bin count matrix.
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
459
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
460 This function is used to generate and add a cell by bin count matrix to the AnnData object.
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
461
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
462 `import_data` must be ran first in order to use this function.
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
463
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
464 More details on the `SnapATAC2 documentation
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
465 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.add_tile_matrix.html>`__
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
466
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
467 A quick-and-dirty way to get marker regions, using `tl.marker_regions`
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
468 ======================================================================
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
469
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
470 A quick-and-dirty way to get marker regions.
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
471
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
472 More details on the `SnapATAC2 documentation
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
473 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.tl.marker_regions.html>`__
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
474
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
475 Identify differentially accessible regions, using `tl.diff_test`
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
476 ====================================================================
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
477
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
478 Identify differentially accessible regions.
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
479
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
480 More details on the `SnapATAC2 documentation
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
481 <https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.tl.diff_test.html>`__
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
482 ]]></help>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
483 <expand macro="citations"/>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
484 </tool>
1c52ce622590 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
iuc
parents:
diff changeset
485