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annotate parse.xml @ 1:43b10ccf53b6 draft

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planemo upload for repository https://github.com/open2c/pairtools commit dcee7286748c82b3f046d9a908bb9ef6365718cf
author iuc
date Mon, 10 Mar 2025 09:35:28 +0000
parents 3b5ee2bf3679
children d8e28fa369e1
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3b5ee2bf3679 planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
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1 <tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" 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[
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8 pairtools parse
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9 '$sam_path'
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10 -c '$chroms_path'
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11 #if str($assembly_name).strip():
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12 --assembly '$assembly_name'
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13 #end if
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14 -o '$output_parsed_pairs'
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15 --min-mapq '$min_mapq'
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16 --max-molecule-size '$max_molecule_size'
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17 $drop_readid
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18 $drop_seq
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19 $output_stats
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20 $drop_sam
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21 #if $output_stats:
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22 '$parsed_pairs_stats'
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23 #end if
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24 --walks-policy '$walks_policy'
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25 --max-inter-align-gap '$max_inter_algn_gap'
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26 --nproc-in \${GALAXY_SLOTS:-4}
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27 --nproc-out \${GALAXY_SLOTS:-4}
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28 ]]></command>
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29 <inputs>
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30 <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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31 <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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32 <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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33 <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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34 <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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35 <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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36 <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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37 <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Generate various statistics of pairs file"></param>
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38 <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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39 <param argument="--walks-policy" type="select" label="Walks Policy" help="The policy for reporting unrescuable walks.">
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40 <expand macro="walks_policy_options"/>
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41 </param>
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42 <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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43 </inputs>
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44 <outputs>
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45 <data name="output_parsed_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: .pairs"/>
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46 <data name="parsed_pairs_stats" format="txt,tabular" label="${tool.name} on ${on_string}: parsed.stats">
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47 <filter>output_stats</filter>
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48 </data>
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49 </outputs>
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50 <tests>
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51 <!--Test 01 with SAM file as input and default parameters-->
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52 <test expect_num_outputs="1">
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53 <param name="sam_path" value="test.sam"/>
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54 <param name="chroms_path" value="test.genome"/>
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55 <param name="min_mapq" value="1"/>
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56 <param name="walks_policy" value="mask"/>
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57 <param name="max_inter_algn_gap" value="20"/>
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58 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_sam.pairs" lines_diff="10"/>
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59 </test>
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60 <!--Test 02 with BAM file as input and default parameters-->
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61 <test expect_num_outputs="1">
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62 <param name="sam_path" value="test.bam"/>
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63 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
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64 <param name="min_mapq" value="1"/>
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65 <param name="walks_policy" value="mask"/>
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66 <param name="max_inter_algn_gap" value="20"/>
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67 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam.pairs" lines_diff="10"/>
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68 </test>
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69 <!--Test 03 with BAM file as input and minimal mapq of 40-->
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70 <test expect_num_outputs="1">
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71 <param name="sam_path" value="test.bam"/>
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72 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
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73 <param name="min_mapq" value="40"/>
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74 <param name="walks_policy" value="mask"/>
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75 <param name="max_inter_algn_gap" value="20"/>
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76 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_min_mapq_40.pairs" lines_diff="10"/>
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77 </test>
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78 <!--Test 04 with BAM file as input and walk policy of 5unique-->
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79 <test expect_num_outputs="1">
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80 <param name="sam_path" value="test.bam"/>
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81 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
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82 <param name="min_mapq" value="40"/>
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83 <param name="walks_policy" value="5unique"/>
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84 <param name="max_inter_algn_gap" value="20"/>
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85 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_5unique.pairs" lines_diff="10"/>
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86 </test>
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87 <!--Test 05 with BAM file as input and read id dropped-->
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88 <test expect_num_outputs="1">
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89 <param name="sam_path" value="test.bam"/>
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90 <param name="chroms_path" value="test.reduced.chrom.sizes"/>
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91 <param name="min_mapq" value="40"/>
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92 <param name="walks_policy" value="5unique"/>
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93 <param name="max_inter_algn_gap" value="20"/>
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94 <param name="drop_readid" value="true"></param>
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95 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_readid_dropped.pairs" lines_diff="10"/>
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96 </test>
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97 <!--Test 06 with SAM file as input and drop_seq enabled-->
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98 <test expect_num_outputs="1">
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99 <param name="sam_path" value="test.sam"/>
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100 <param name="chroms_path" value="test.genome"/>
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101 <param name="min_mapq" value="40"/>
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102 <param name="walks_policy" value="5unique"/>
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103 <param name="max_inter_algn_gap" value="20"/>
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104 <param name="drop_seq" value="true"></param>
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105 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_bam_readid_dropped_seq.pairs" lines_diff="10"/>
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106 </test>
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107 <!--Test 07 with SAM file as input and output_stats enabled-->
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108 <test expect_num_outputs="2">
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109 <param name="sam_path" value="test.sam"/>
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110 <param name="chroms_path" value="test.genome"/>
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111 <param name="min_mapq" value="40"/>
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112 <param name="walks_policy" value="5unique"/>
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113 <param name="max_inter_algn_gap" value="20"/>
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114 <param name="output_stats" value="true"></param>
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115 <output name="parsed_pairs_stats" file="output_parsed_pairs.stats" lines_diff="10"/>
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116 </test>
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117 <!--Test 08 with SAM file as input and default parameters and assembly name -->
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118 <test expect_num_outputs="1">
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119 <param name="sam_path" value="test.sam"/>
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120 <param name="chroms_path" value="test.genome"/>
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121 <param name="assembly_name" value="test_assembly"/>
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122 <param name="min_mapq" value="1"/>
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123 <param name="walks_policy" value="mask"/>
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124 <param name="max_inter_algn_gap" value="20"/>
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125 <output name="output_parsed_pairs" ftype="4dn_pairs" file="output_parsed_pairs_sam_assemblyname.pairs" lines_diff="10"/>
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126 </test>
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127
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128 </tests>
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129 <help><![CDATA[
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130 **Pairtools parse**
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131
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132 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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133
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134 sam_path : an input .sam/.bam (unsorted/name-sorted) file with paired-end sequence alignments of Hi-C molecules.
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135
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136 ]]></help>
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137 <expand macro="citations"/>
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138 <expand macro="creator"/>
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139 </tool>