Mercurial > repos > iuc > hicstuff_pipeline

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff commit 07701847a3c4d66ee12cecd37b5129ed6984082a
author iuc
date Thu, 10 Oct 2024 17:26:14 +0000
parents 6956f0783d77
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1 <tool id="hicstuff_pipeline" name="hicstuff full pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>generates a Hi-C contact matrix</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 hicstuff pipeline
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10 --genome '$genome'
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11 --outdir results
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12 --aligner $aligner
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13 $circular
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14 $duplicates
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15 --enzyme '$enzyme'
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16 $filter
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17 --mapping $mapping
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18 --matfmt $matfmt
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19 --quality-min $quality_min
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20 --size $size
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21 --threads "\${GALAXY_SLOTS:-1}"
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22 #if $paired_cond.paired_select == "paired"
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23 '$paired_cond.reads.forward'
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24 '$paired_cond.reads.reverse'
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25 #else
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26 '$forward_reads'
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27 '$reverse_reads'
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28 #end if
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29 ]]></command>
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30 <inputs>
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31 <param type="data" name="genome" format="fasta,fasta.gz" label="Genome fasta file"/>
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32 <conditional name="paired_cond">
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33 <param name="paired_select" type="select" label="Paired reads">
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34 <option value="paired">In a dataset pair</option>
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35 <option value="separate">In two separate datasets</option>
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36 </param>
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37 <when value="paired">
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38 <param name="reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Paired reads"/>
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39 </when>
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40 <when value="separate">
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41 <param name="forward_reads" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads"/>
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42 <param name="reverse_reads" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads"/>
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43 </when>
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44 </conditional>
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45 <param argument="--aligner" type="select" label="Alignment software to use" help="Minimap2 should only be used for reads > 100 bp">
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46 <option value="bowtie2" selected="true">bowtie2</option>
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47 <option value="minimap2">minimap2</option>
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48 <option value="bwa">bwa</option>
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49 </param>
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50 <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" label="Circular genome"/>
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51 <param argument="--duplicates" type="boolean" truevalue="--duplicates" falsevalue="" label="Removes PCR duplicates" help="PCR duplicates are defined as sets of pairs having identical mapping positions for both reads."/>
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52 <param argument="--enzyme" type="text" value="5000" label="Bin size or enzyme" help="Restriction enzyme or 'mnase' if a string, or chunk size (i.e. resolution) if a number. Can also be multiple comma-separated enzymes."/>
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53 <param argument="--filter" type="boolean" truevalue="--filter" falsevalue="" label="Filters out spurious 3C events, such as self religations or undigested fragments" help="This is only really useful at very fine resolutions (1-2kb) and not needed most of the time. This option is only meaningful when --enzyme is given a restriction enzyme and not a bin size."/>
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54 <param argument="--mapping" type="select" label="Parameter of mapping" help="'normal': Directly map reads without any process. 'iterative': Map reads iteratively using iteralign, by truncating reads to 20bp and then repeatedly extending to align them. 'cutsite': Cut reads at the religation sites of the given enzyme using cutsite, create new pairs of reads and then align them ; enzyme is required">
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55 <option value="normal" selected="true">normal</option>
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56 <option value="iterative">iterative</option>
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57 <option value="cutsite">cutsite</option>
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58 </param>
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59 <param argument="--matfmt" type="select" label="Format of the output sparse matrix" help="Available formats are bg2 (bedgraph2d), graal (graal-compatible plain text COO format) and cool, a binary format that is probably the most appropriate for large genomes.">
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60 <option value="bg2">bg2</option>
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61 <option value="cool">cool</option>
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62 <option value="graal" selected="true">graal</option>
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63 </param>
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64 <param argument="--quality-min" type="integer" value="30" label="Minimum mapping quality for selecting contacts"/>
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65 <param argument="--size" type="integer" value="0" label="Minimum size threshold to consider contigs. Keep all contigs by default."/>
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66 </inputs>
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67 <outputs>
1
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68 <data name="abs_fragments_contacts_weighted_graal" from_work_dir="./results/abs_fragments_contacts_weighted.txt" format="tabular" label="${tool.name} on ${on_string}: Contact matrix (graal)">
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69 <filter>matfmt == "graal"</filter>
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70 </data>
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71 <data name="abs_fragments_contacts_weighted_bg2" from_work_dir="./results/abs_fragments_contacts_weighted.bg2" format="tabular" label="${tool.name} on ${on_string}: Contact matrix (bg2)">
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72 <filter>matfmt == "bg2"</filter>
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73 </data>
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74 <data name="abs_fragments_contacts_weighted_cool" from_work_dir="./results/abs_fragments_contacts_weighted.cool" format="cool" label="${tool.name} on ${on_string}: Contact matrix (cool)">
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75 <filter>matfmt == "cool"</filter>
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76 </data>
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77 <data name="fragments_list" from_work_dir="./results/fragments_list.txt" format="tabular" label="${tool.name} on ${on_string}: Fragment list"/>
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78 <data name="info_contigs" from_work_dir="./results/info_contigs.txt" format="tabular" label="${tool.name} on ${on_string}: Contig info"/>
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79 </outputs>
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80 <tests>
1
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81 <test expect_num_outputs="3">
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82 <param name="genome" value="seq.fa.gz" />
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83 <param name="paired_cond|paired_select" value="separate"/>
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84 <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" />
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85 <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz" />
1
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86 <output name="abs_fragments_contacts_weighted_graal">
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87 <assert_contents>
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88 <has_n_lines n="77"/>
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89 <has_n_columns n="3"/>
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90 </assert_contents>
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91 </output>
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92 <output name="fragments_list">
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93 <assert_contents>
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94 <has_n_lines n="17"/>
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95 <has_n_columns n="6"/>
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96 </assert_contents>
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97 </output>
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98 <output name="info_contigs" file="info_contigs.txt"/>
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99 <assert_stderr>
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100 <has_text text="Contact map generated" />
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101 </assert_stderr>
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102 </test>
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103 <!-- bg2 format -->
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104 <test expect_num_outputs="3">
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105 <param name="genome" value="seq.fa.gz" />
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106 <param name="paired_cond|paired_select" value="separate"/>
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107 <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" />
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108 <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz" />
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109 <param name="matfmt" value="bg2"/>
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110 <output name="abs_fragments_contacts_weighted_bg2">
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111 <assert_contents>
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112 <has_n_lines n="76"/>
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113 <has_n_columns n="7"/>
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114 </assert_contents>
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115 </output>
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116 <output name="fragments_list">
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117 <assert_contents>
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118 <has_n_lines n="17"/>
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119 <has_n_columns n="6"/>
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120 </assert_contents>
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121 </output>
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122 <output name="info_contigs" file="info_contigs.txt"/>
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123 <assert_stderr>
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124 <has_text text="Contact map generated" />
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125 </assert_stderr>
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126 </test>
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127 <!-- cool format -->
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128 <test expect_num_outputs="3">
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129 <param name="genome" value="seq.fa.gz" />
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130 <param name="paired_cond|paired_select" value="separate"/>
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131 <param name="paired_cond|forward_reads" value="sample.reads_for.fastq.gz" />
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132 <param name="paired_cond|reverse_reads" value="sample.reads_rev.fastq.gz" />
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133 <param name="matfmt" value="cool"/>
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134 <output name="abs_fragments_contacts_weighted_cool">
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135 <assert_contents>
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136 <has_h5_keys keys="bins,chroms,indexes,pixels"/>
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137 </assert_contents>
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138 </output>
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139 <output name="fragments_list">
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140 <assert_contents>
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141 <has_n_lines n="17"/>
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142 <has_n_columns n="6"/>
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143 </assert_contents>
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144 </output>
0
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145 <output name="info_contigs" file="info_contigs.txt"/>
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146 <assert_stderr>
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147 <has_text text="Contact map generated" />
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148 </assert_stderr>
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149 </test>
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150 </tests>
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151 <help><![CDATA[
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152
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153 hicstuff is a toolkit to generate and manipulate Hi-C matrices.
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154
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155 The "hicstuff full pipeline" tool generates a Hi-C contact matrix.
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156 Output files can be used with instaGRAAL downstream.
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157
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158 -----------
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159 Input files
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160 -----------
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161 * the fasta genome file
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162 * forward reads
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163 * reverse reads
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164
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165 ------------
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166 Output files
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167 ------------
1
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168 * Contact matrix: Sparse matrix file with 3 columns the rows, column and values of nonzero pixels. The first row contains the shape and total number of nonzero pixels in the matrix.
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169 * Fragment ist: Contains genomic coordinates of the matrix bins (row/columns).
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170 * Contig info.txt: Contains chromosome names, theirs length and number of bins.
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171
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172 ]]></help>
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173 <expand macro="citations" />
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174 </tool>