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planemo upload for repository https://github.com/open2c/pairtools commit f60e7663dc3fd1a564e691ef35d35f35b0a851ad
author iuc
date Wed, 24 Sep 2025 11:48:55 +0000
parents d8e28fa369e1
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1 <tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" license="MIT">
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2 <description>Find ligation pairs in alignments and create pairs.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
2
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8 #set $output = "output" + str($compress_output)
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9 ln -s '$output_parsed_pairs' '$output' &&
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10 pairtools parse
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11 '$sam_path'
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12 -c '$chroms_path'
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13 #if str($assembly_name).strip():
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14 --assembly '$assembly_name'
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15 #end if
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16 --min-mapq '$min_mapq'
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17 --max-molecule-size '$max_molecule_size'
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18 $drop_readid
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19 $drop_seq
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20 $drop_sam
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21 #if $output_stats:
2
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22 --output-stats '$parsed_pairs_stats'
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23 #end if
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24 #if $select_add_columns.add_columns_selection == "yes":
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25 --add-columns '$select_add_columns.add_columns'
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26 #end if
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27 --walks-policy '$walks_policy'
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28 --max-inter-align-gap '$max_inter_algn_gap'
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29 --nproc-in \${GALAXY_SLOTS:-4}
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30 --nproc-out \${GALAXY_SLOTS:-4}
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31 #if $sort_output:
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32 |
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33 pairtools sort -o '$output'
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34 --nproc-in \${GALAXY_SLOTS:-4}
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35 --nproc-out \${GALAXY_SLOTS:-4}
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36 #else
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37 -o '$output'
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38 #end if
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39
0
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40 ]]></command>
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41 <inputs>
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42 <param name="sam_path" type="data" format="sam,qname_input_sorted.bam,qname_sorted.bam" label="Input SAM/BAM file" help="Input SAM or BAM (unsorted/name-sorted) file with paired-end sequence alignments of Hi-C molecules."/>
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43 <param name="chroms_path" argument="-c" type="data" format="tabular" label="Input a chromosome order file" help="Chromosome order used to flip interchromosomal mates. Any scaffolds not listed will be ordered lexicographically."/>
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44 <param name="assembly_name" type="text" value="" label="Input a name of genome assembly" help="Name of genome assembly (e.g. hg19, mm10) to store in the pairs header"></param>
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45 <param argument="--min-mapq" type="integer" value="40" min="0" label="Minimal MAPQ" help="Minimal MAPQ score to consider a read as uniquely mapped."/>
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46 <param argument="--max-molecule-size" type="integer" min="0" value="750" label="Input the maximal size of a Hi-C molecule" help="The maximal size of a Hi-C molecule; used to rescue single ligations(from molecules with three alignments) and to rescue complex ligations."></param>
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47 <param argument="--drop-readid" type="boolean" truevalue="--drop-readid" falsevalue="" checked="False" label="Do not add read ids to the output"></param>
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48 <param argument="--drop-seq" type="boolean" truevalue="--drop-seq" falsevalue="" checked="False" label="remove sequences and PHREDs from the sam fields"></param>
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49 <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Generate various statistics of pairs file"></param>
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50 <param argument="--drop-sam" type="boolean" truevalue="--drop-sam" falsevalue="" checked="False" label="Do not add sams to the output"></param>
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51 <conditional name="select_add_columns">
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52 <param name="add_columns_selection" type="select" label="Add additional columns to the output" help="Select if additional columns needs to be added to the output pairs file.">
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53 <option value="no" selected="true">No</option>
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54 <option value="yes">Yes</option>
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55 </param>
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56 <when value="yes">
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57 <param argument="--add-columns" type="select" multiple="true" label="Select extra columns describing alignments" help="Multiple options can be selected.">
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58 <option value="mapq">MAPQ</option>
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59 <option value="pos5">POS5</option>
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60 <option value="pos3">POS3</option>
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61 <option value="cigar">CIGAR</option>
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62 <option value="read_len">Read length</option>
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63 <option value="matched_bp">Matched bp</option>
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64 <option value="algn_ref_span">algn_ref_span</option>
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65 <option value="dist_to_5">dist_to_5</option>
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66 <option value="dist_to_3">dist_to_3</option>
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67 <option value="seq">seq</option>
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68 <option value="mismatches">mismatches</option>
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69 <option value="read_side">read_side</option>
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70 <option value="algn_idx">algn_idx</option>
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71 <option value="same_side_algn_count">same_side_algn_count</option>
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72 </param>
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73 </when>
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74 <when value="no"/>
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75 </conditional>
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76 <param argument="--walks-policy" type="select" label="Walks Policy" help="The policy for reporting unrescuable walks.">
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77 <expand macro="walks_policy_options"/>
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78 </param>
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79 <param name="compress_output" type="boolean" truevalue=".gz" falsevalue="" checked="false" label="Compress output file" />
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80 <param name="sort_output" type="boolean" checked="true" label="generate sorted output file" />
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81 <param argument="max_inter_algn_gap" type="integer" min="0" value="30" label="Max alignment gap" help="read segments that are not covered by any alignment and longer than the specified value are treated as null alignments."/>
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82 </inputs>
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83 <outputs>
2
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84 <data name="output_parsed_pairs" format="4dn_pairsam" label="${tool.name} on ${on_string}: .pairs">
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85 <change_format>
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86 <when input="compress_output" value=".gz" format="4dn_pairsam.gz"/>
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87 </change_format>
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88 </data>
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89 <data name="parsed_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: parsed.stats">
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90 <filter>output_stats</filter>
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91 </data>
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92 </outputs>
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93 <tests>
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94 <!--Test 01 with SAM file as input and default parameters-->
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95 <test expect_num_outputs="1">
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96 <param name="sam_path" value="test.sam"/>
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97 <param name="chroms_path" value="test.genome"/>
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98 <param name="min_mapq" value="1"/>
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99 <param name="walks_policy" value="mask"/>
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100 <param name="max_inter_algn_gap" value="20"/>
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101 <param name="sort_output" value="false"/>
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102 <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam.pairs" lines_diff="10"/>
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103 </test>
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104 <!--Test 02 with SAM file as input and sorted output default parameters-->
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105 <test expect_num_outputs="1">
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106 <param name="sam_path" value="test.sam"/>
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107 <param name="chroms_path" value="test.genome"/>
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108 <param name="min_mapq" value="1"/>
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109 <param name="walks_policy" value="mask"/>
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110 <param name="max_inter_algn_gap" value="20"/>
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111 <param name="sort_output" value="true"/>
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112 <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam.sorted.pairs" lines_diff="10"/>
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113 </test>
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114 <!--Test 03 with BAM file as input and default parameters-->
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115 <test expect_num_outputs="1">
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116 <param name="sam_path" value="test.bam"/>
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117 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
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118 <param name="min_mapq" value="1"/>
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119 <param name="walks_policy" value="mask"/>
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120 <param name="max_inter_algn_gap" value="20"/>
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121 <param name="sort_output" value="false"/>
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122 <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam.pairs" lines_diff="10"/>
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123 </test>
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124 <!--Test 04 with BAM file as input and minimal mapq of 40-->
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125 <test expect_num_outputs="1">
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126 <param name="sam_path" value="test.bam"/>
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127 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
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128 <param name="min_mapq" value="40"/>
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129 <param name="walks_policy" value="mask"/>
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130 <param name="max_inter_algn_gap" value="20"/>
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131 <param name="sort_output" value="false"/>
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132 <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_min_mapq_40.pairs" lines_diff="10"/>
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133 </test>
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134 <!--Test 05 with BAM file as input and walk policy of 5unique-->
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135 <test expect_num_outputs="1">
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136 <param name="sam_path" value="test.bam"/>
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137 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
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138 <param name="min_mapq" value="40"/>
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139 <param name="walks_policy" value="5unique"/>
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140 <param name="max_inter_algn_gap" value="20"/>
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141 <param name="sort_output" value="false"/>
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142 <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_5unique.pairs" lines_diff="10"/>
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143 </test>
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144 <!--Test 06 with BAM file as input and read id dropped-->
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145 <test expect_num_outputs="1">
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146 <param name="sam_path" value="test.bam"/>
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147 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
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148 <param name="min_mapq" value="40"/>
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149 <param name="walks_policy" value="5unique"/>
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150 <param name="max_inter_algn_gap" value="20"/>
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151 <param name="drop_readid" value="true"></param>
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152 <param name="sort_output" value="false"/>
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153 <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_readid_dropped.pairs" lines_diff="10"/>
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154 </test>
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155 <!--Test 07 with SAM file as input and drop_seq enabled-->
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156 <test expect_num_outputs="1">
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157 <param name="sam_path" value="test.sam"/>
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158 <param name="chroms_path" value="test.genome"/>
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159 <param name="min_mapq" value="40"/>
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160 <param name="walks_policy" value="5unique"/>
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161 <param name="max_inter_algn_gap" value="20"/>
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162 <param name="drop_seq" value="true"></param>
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163 <param name="sort_output" value="false"/>
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164 <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_bam_readid_dropped_seq.pairs" lines_diff="10"/>
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165 </test>
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166 <!--Test 08 with SAM file as input and output_stats enabled-->
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167 <test expect_num_outputs="2">
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168 <param name="sam_path" value="test.sam"/>
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169 <param name="chroms_path" value="test.genome"/>
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170 <param name="min_mapq" value="40"/>
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171 <param name="walks_policy" value="5unique"/>
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172 <param name="max_inter_algn_gap" value="20"/>
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173 <param name="output_stats" value="true"></param>
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174 <output name="parsed_pairs_stats" file="output_parsed_pairs.stats" lines_diff="10"/>
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175 </test>
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176 <!--Test 09 with SAM file as input and default parameters and assembly name -->
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177 <test expect_num_outputs="1">
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178 <param name="sam_path" value="test.sam"/>
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179 <param name="chroms_path" value="test.genome"/>
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180 <param name="assembly_name" value="test_assembly"/>
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181 <param name="min_mapq" value="1"/>
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182 <param name="walks_policy" value="mask"/>
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183 <param name="max_inter_algn_gap" value="20"/>
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184 <param name="sort_output" value="false"/>
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185 <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam_assemblyname.pairs" lines_diff="10"/>
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186 </test>
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187 <!--Test 10 with SAM file as input and default parameters and assembly name and compressed output-->
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188 <test expect_num_outputs="1">
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189 <param name="sam_path" value="test.sam"/>
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190 <param name="chroms_path" value="test.genome"/>
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191 <param name="assembly_name" value="test_assembly"/>
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192 <param name="min_mapq" value="1"/>
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193 <param name="walks_policy" value="mask"/>
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194 <param name="max_inter_algn_gap" value="20"/>
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195 <param name="compress_output" value="true"/>
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196 <param name="sort_output" value="false"/>
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197 <output name="output_parsed_pairs" ftype="4dn_pairsam.gz" file="output_parsed_pairs_sam_assemblyname.pairs.gz" decompress="true" lines_diff="10"/>
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198 </test>
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199 <!--Test 11 with SAM file as input and default parameters and assembly name and sorted, compressed output-->
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200 <test expect_num_outputs="1">
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201 <param name="sam_path" value="test.sam"/>
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202 <param name="chroms_path" value="test.genome"/>
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203 <param name="assembly_name" value="test_assembly"/>
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204 <param name="min_mapq" value="1"/>
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205 <param name="walks_policy" value="mask"/>
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206 <param name="max_inter_algn_gap" value="20"/>
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207 <param name="compress_output" value="true"/>
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208 <output name="output_parsed_pairs" ftype="4dn_pairsam.gz" file="output_parsed_pairs_sam_assemblyname.sorted.pairs.gz" decompress="true" lines_diff="10"/>
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209 </test>
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210 <!--Test 12 with SAM file as input and add columns-->
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211 <test expect_num_outputs="1">
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212 <param name="sam_path" value="test.sam"/>
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213 <param name="chroms_path" value="test.genome"/>
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214 <param name="min_mapq" value="1"/>
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215 <param name="walks_policy" value="mask"/>
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216 <param name="max_inter_algn_gap" value="20"/>
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217 <conditional name="select_add_columns">
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218 <param name="add_columns_selection" value="yes"/>
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219 <param name="add_columns" value="mapq,seq"/>
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220 </conditional>
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221 <param name="sort_output" value="false"/>
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222 <output name="output_parsed_pairs" ftype="4dn_pairsam" file="output_parsed_pairs_sam_mapq.pairs" lines_diff="10"/>
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223 </test>
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224 </tests>
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225 <help><![CDATA[
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226 **Pairtools parse**
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227
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228 Detects ligation events in the aligned sequences of DNA molecules formed in Hi-C experiments and reports them in the .pairs/.pairsam format.
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229
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230 sam_path : an input .sam/.bam (unsorted/name-sorted) file with paired-end sequence alignments of Hi-C molecules.
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231
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232 By default, the generated .pair/.pairsam output is sorted by piping it through pairtools sort. You can disable this behavior by unchecking the “Generate sorted output file” checkbox.
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233
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234 ]]></help>
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235 <expand macro="citations"/>
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236 <expand macro="creator"/>
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237 </tool>