Mercurial > repos > iuc > snapatac2_clustering

annotate macros.xml @ 4:afb90d3485df draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 04112de6f91d4f848fe35d857c84c4b8a9fc980f
author iuc
date Tue, 23 Jul 2024 16:24:56 +0000
parents 509baa4a2da0
children
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af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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1 <macros>
3
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2 <token name="@TOOL_VERSION@">2.6.4</token>
4
afb90d3485df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 04112de6f91d4f848fe35d857c84c4b8a9fc980f
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3 <token name="@VERSION_SUFFIX@">1</token>
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4 <token name="@PROFILE@">23.0</token>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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5 <xml name="requirements">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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6 <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement>
3
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7 <requirement type="package" version="5.22.0">plotly</requirement>
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8 <requirement type="package" version="0.2.1">python-kaleido</requirement>
3
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9 <requirement type="package" version="1.1.0">polars</requirement>
509baa4a2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
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10 <requirement type="package" version="16.1.0">pyarrow</requirement>
509baa4a2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
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11 <requirement type="package" version="0.11.6">python-igraph</requirement>
509baa4a2da0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit b37248ea9b492c096b143272aebc79d8f04c2984
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12 <requirement type="package" version="0.8.37">hdbscan</requirement>
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13 <requirement type="package" version="0.0.10">harmonypy</requirement>
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14 <requirement type="package" version="1.7.4">scanorama</requirement>
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15 <requirement type="package" version="3.0.1">macs3</requirement>
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16 <requirement type="package" version="0.70.16">multiprocess</requirement>
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17 <requirement type="package" version="0.10.2">leidenalg</requirement>
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18 <yield />
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19 </xml>
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21 <token name="@PREP_ADATA@"><![CDATA[
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22 cp '$method.adata' 'anndata.h5ad' &&
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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23 ]]>
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24 </token>
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26 <token name="@CMD@"><![CDATA[
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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27 cat '$script_file' > '$hidden_output' &&
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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28 python '$script_file' >> '$hidden_output' &&
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29 touch 'anndata_info.txt' &&
8f8bef61fd0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f
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30 cat 'anndata_info.txt' @CMD_prettify_stdout@
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af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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31 ]]>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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32 </token>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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34 <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g" | sed -r 's|^\s*(.*):\s(.*)|[\1]\n- \2|g' | sed 's|, |\n- |g'
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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35 ]]></token>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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37 <token name="@CMD_imports@"><![CDATA[
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38 import snapatac2 as sa
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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39 import os
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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40 ]]>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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41 </token>
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42 <xml name="sanitize_query" token_validinitial="string.printable">
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43 <sanitizer>
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44 <valid initial="@VALIDINITIAL@">
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45 <remove value="&apos;" />
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46 </valid>
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47 </sanitizer>
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48 </xml>
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49
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50 <xml name="inputs_anndata">
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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51 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
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52 </xml>
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53
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54 <token name="@CMD_read_inputs@"><![CDATA[
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55
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56 adata = sa.read('anndata.h5ad', backed = None)
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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57 ]]>
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58 </token>
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59
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60 <xml name="dimentions_plot">
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61 <param argument="width" type="integer" value="500" label="Width of the plot"/>
1
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62 <param argument="height" type="integer" value="400" label="Height of the plot"/>
0
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63 </xml>
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64
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65 <xml name="param_groupby">
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66 <param argument="groupby" type="text" label="The key of the observation grouping to consider">
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67 <expand macro="sanitize_query" />
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68 </param>
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69 </xml>
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70
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71 <xml name="out_file">
1
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72 <param name="out_file" type="select" optional="true" label="Type of output plot">
0
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73 <option value="png" selected="true">PNG</option>
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74 <option value="svg">SVG</option>
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75 <option value="pdf">PDF</option>
1
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76 </param>
0
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77 </xml>
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78 <token name="@CMD_anndata_write_outputs@"><![CDATA[
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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79 adata.write('anndata.h5ad')
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80 with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
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81 print(adata, file=ainfo)
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82 ]]>
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83 </token>
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84 <xml name="inputs_common_advanced">
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85 <section name="advanced_common" title="Advanced Options" expanded="false">
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86 <param name="show_log" type="boolean" checked="false" label="Output Log?" />
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87 </section>
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88 </xml>
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89 <xml name="params_render_plot">
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90 <param argument="width" type="integer" value="600" label="Width of the plot"/>
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91 <param argument="height" type="integer" value="400" label="Height of the plot"/>
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92 <expand macro="out_file"/>
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93 </xml>
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94 <xml name="param_shift">
1
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95 <param argument="shift_left" type="integer" value="4" label="Insertion site correction for the left end" help="Note this has no effect on single-end reads"/>
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96 <param argument="shift_right" type="integer" value="-5" label="Insertion site correction for the right end" help="Note this has no effect on single-end reads"/>
0
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97 </xml>
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98 <xml name="param_chunk_size" tokens="size">
1
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99 <param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/>
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100 </xml>
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101 <xml name="min_max_frag_size">
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102 <param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/>
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103 <param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/>
0
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104 </xml>
1
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105 <xml name="params_data_integration">
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106 <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/>
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107 <param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation">
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108 <expand macro="sanitize_query"/>
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109 </param>
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110 <param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider">
0
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111 <expand macro="sanitize_query" />
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112 </param>
1
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113 <param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/>
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114 </xml>
0
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115 <xml name="param_n_comps">
1
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116 <param argument="n_comps" type="integer" value="30" label="Number of dimensions to keep" help="The result is insensitive to this parameter when `weighted_by_sd` is set, as long as it is large enough, e.g. 30."/>
0
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117 </xml>
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118 <xml name="param_random_state">
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119 <param argument="random_state" type="integer" value="0" label="Seed of the random state generator"/>
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120 </xml>
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121 <xml name="param_key_added" tokens="key_added">
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122 <param argument="key_added" type="text" value="@KEY_ADDED@" label="`adata.obs` key under which t add cluster labels"/>
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123 </xml>
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124 <xml name="param_use_rep">
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125 <param argument="use_rep" type="text" value="X_spectral" label="Use the indicated representation in `.obsm`"/>
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126 </xml>
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127 <xml name="genome_fasta">
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128 <param argument="genome_fasta" type="text" label="A fasta file containing the genome sequences or a Genome object"/>
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129 </xml>
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130 <xml name="background">
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131 <param argument="background" type="text" optional="true" value="" label="A list of regions to be used as the background">
1
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132 <expand macro="sanitize_query"/>
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133 </param>
0
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134 </xml>
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135 <xml name="mat">
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136 <param argument="peak_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by peak count matrix"/>
1
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137 <param argument="gene_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by gene count matrix"/>
0
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138 </xml>
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139 <xml name="param_network">
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140 <param argument="network" type="text" label="network"/>
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141 </xml>
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142 <xml name="param_n_iterations">
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143 <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform"
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144 help="Positive values above 2 define the total number of iterations to perform, -1 has the algorithm run until it reaches its optimal clustering."/>
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145 </xml>
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146
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147 <xml name="citations">
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148 <citations>
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149 <citation type="doi">10.1038/s41592-023-02139-9</citation>
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150 </citations>
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151 </xml>
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152 <xml name="render_plot_test">
1
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153 <param name="width" value="650"/>
0
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154 <param name="height" value="450"/>
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155 </xml>
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156 <xml name="render_plot_matching_text">
1
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157 <has_text_matching expression="width = 650"/>
0
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158 <has_text_matching expression="height = 450"/>
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159 </xml>
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160 <xml name="param_counting_strategy">
3
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161 <param argument="counting_strategy" type="select" label="The strategy to compute feature counts">
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162 <option value="fragment">"fragment": based on the number of fragments that overlap with a region of interest</option>
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163 <option value="insertion" selected="true">"insertion": based on the number of insertions that overlap with a region of interest</option>
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164 <option value="paired-insertion">"paired-insertion": similar to "insertion", but it only counts the insertions once if the pair of insertions of a fragment are both within the same region of interest</option>
0
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165 </param>
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166 </xml>
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167
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168 <token name="@CMD_params_data_integration@"><![CDATA[
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169 use_rep = '$method.use_rep',
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170 #if $method.use_dims != ''
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171 #set $dims = ([x.strip() for x in str($method.use_dims).split(',')])
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172 use_dims=$dims,
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173 #end if
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174 #if $method.groupby != ''
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175 #set $groupby = ([x.strip() for x in str($method.groupby).split(',')])
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176 groupby=$groupby,
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177 #end if
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178 #if $method.key_added != ''
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179 key_added = '$method.key_added',
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180 #end if
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181 ]]>
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182 </token>
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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183
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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184 <token name="@CMD_params_render_plot@"><![CDATA[
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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185 width = $method.width,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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186 height = $method.height,
af821711b356 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit be132b56781bede5dc6e020aa80ca315546666cd
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187 out_file = 'plot.$method.out_file',
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188 ]]>
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189 </token>
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190 </macros>