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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit ab918ac1eab72932e78c6e45e46d745543eac810
author iuc
date Wed, 17 Sep 2025 06:27:53 +0000
parents d802668bc0fe
children
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1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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1 <tool id="yahs" name="YAHS" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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2 <description>yet another HI-C scaffolding tool</description>
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3 <macros>
3
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4 <token name="@VERSION@">1.2a.2</token>
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5 <token name="@VERSION_SUFFIX@">3</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@VERSION@">yahs</requirement>
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9 <requirement type="package" version="1.11">samtools</requirement>
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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10 <requirement type="package" version="3.9">python</requirement>
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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13 #if $function.function_select == "yahs":
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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14 ln -s '$function.fasta' input.fasta &&
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15 ln -s '$function.bfile' input.$function.bfile.ext &&
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16 #if $function.agp:
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17 ln -s '$function.agp' input.agp &&
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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18 #end if
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19 samtools faidx input.fasta &&
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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20 mkdir initial_break agp_out agp_break final_outs &&
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21 yahs --no-mem-check input.fasta input.$function.bfile.ext
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22 #if $agp:
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23 -a input.agp
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24 #end if
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25 #if $function.res:
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26 -r $function.res
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27 #end if
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28 #if $function.enzyme_conditional.enzyme_options == 'preconfigured':
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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29 #if $function.enzyme_conditional.preconfigured_enzymes == 'dovetail'
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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30 -e 'GATC'
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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31 #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima1'
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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32 -e 'GATC,GANTC'
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33 #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima2'
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34 -e 'GATC,GANTC,CTNAG,TTAA'
4
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35 #else if $function.enzyme_conditional.preconfigured_enzymes == 'omnic'
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36
0
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37 #end if
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38 #else if $function.enzyme_conditional.enzyme_options == 'specific':
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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39 -e '${function.enzyme_conditional.manual_enzyme}'
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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40 #end if
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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41 #if $function.length:
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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42 -l $function.length
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43 #end if
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44 #if $function.quality:
1c2056885441 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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45 -q $function.quality
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46 #end if
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47 $function.no_contig_ec
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48 $function.no_scaffold_ec
2
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49 -o yahs_out
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50 #if $log_out
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51 2> output.log
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52 #end if
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53 && ls -lah &&
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54 python '$__tool_directory__/move_files.py'
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55 && ls -lah ./*
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56 #else:
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57 ln -s '$function.fasta' input.fasta &&
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58 ln -s '$function.agp' input.agp &&
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59 agp_to_fasta input.agp input.fasta
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60 #if $function.length:
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61 -l $function.length
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62 #end if
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63 -o output.fasta
2
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64 #if $log_out:
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65 2> output.log
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66 #end if
0
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67 #end if
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68 ]]></command>
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69 <inputs>
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70 <conditional name="function">
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71 <param name="function_select" type="select" label="Which function would you like to run?">
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72 <option value="yahs">YAHS</option>
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73 <option value="agp_to_fasta">AGP to fasta</option>
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74 </param>
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75 <when value="yahs">
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76 <param name="fasta" type="data" format="fasta" label="Input contig sequences"/>
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c4b9b2d57fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit ab918ac1eab72932e78c6e45e46d745543eac810
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77 <param name="bfile" type="data" format="bam,bed,qname_sorted.bam,unsorted.bam" label="Alignment file of Hi-C reads to contigs. NOTE: The input BAM could either be sorted by read names (qname_sorted.bam) or not. The behaviours of the program are slightly different, which might lead to slightly different scaffolding results. For a BAM input sorted by read names, with each mapped read pair, a Hi-C link is counted between the middle positions of the read alignments; while for a BAM input sorted by coordinates or unsorted, Hi-C links are counted between the start positions of the read alignments. Also, for a BAM input not sorted by read names, the mapping quality filtering is suppressed (-q option). If a bed file is provided: the BAM file used to genereate BED file need to be filtered out unmapped reads, supplementary/secondary alignment records, and PCR/optical duplicates, and sorted by read names (otherwise the resulted BED file need to be sorted by the read name column)."/>
c4b9b2d57fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit ab918ac1eab72932e78c6e45e46d745543eac810
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78 <param name="agp" argument="-a" type="data" format="agp" optional="true" label="Input AGP file (for rescaffolding)" help="You can specify a AGP format file to ask YaHS to do scaffolding with the scaffolds in the AGP file as the start point"/>
c4b9b2d57fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit ab918ac1eab72932e78c6e45e46d745543eac810
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79 <param name="res" argument="-r" type="text" label="Resolutions" optional="true" help="Comma separated, ascending list of range of resolutions with no spaces. Ex. 50000,100000,200000,500000,1000000,2000000,5000000. By default and the upper limit is automatically adjusted with the genome size">
c4b9b2d57fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit ab918ac1eab72932e78c6e45e46d745543eac810
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80 <validator type="regex" message="Only Numbers and commas can be used in to define the list of range of resolutions.">^\d+(,\d+)*$</validator>
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81 </param>
0
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82 <conditional name="enzyme_conditional">
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83 <param name="enzyme_options" type="select" label="Restriction enzyme used in Hi-C experiment" help="Hi-C experiments can use different restriction enzymes.
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84 The enzyme frequency in contigs is used to normalize the Hi-C interaction frequency. Note that you need to specify the actual
c4b9b2d57fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit ab918ac1eab72932e78c6e45e46d745543eac810
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85 sequence of the cutting site for a restriction enzyme and not the enzyme name. You can also specify DNASE as an enzyme if you
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86 use an enzyme-free prep, e.g. Omni-C.">
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87 <option value="not_specified">Not specified</option>
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88 <option value="preconfigured">Preconfigured restriction enzymes</option>
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89 <option value="specific">Enter a specific sequence</option>
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90 </param>
2
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91 <when value="not_specified"/>
0
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92 <when value="preconfigured">
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93 <param name="preconfigured_enzymes" argument="-e" type="select" label="Preconfigured enzymes">
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94 <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option>
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95 <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option>
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96 <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option>
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97 <option value="omnic">Dovetail Omni-C: enzyme-free prep</option>
0
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98 </param>
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99 </when>
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100 <when value="specific">
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101 <param name="manual_enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)" help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT').">
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102 <validator type="expression" message="Only alphabetical letters and the comma can be used in to define restriction enzyme sequences.">value.replace(',', '').isalpha()</validator>
0
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103 </param>
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104 </when>
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105 </conditional>
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106 <param name="length" argument="-l" type="integer" label="Minimum contig length included for scaffolding" min="1" optional="true"/>
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107 <param name="quality" argument="-q" type="integer" label="Minimum read mapping quality (for BAM input only)" min="1" optional="true"/>
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108 <param argument="--no-contig-ec" type="boolean" label="Skip assembly error correction step" truevalue="--no-contig-ec" falsevalue="" help="Automatically active if AGP output is set"/>
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109 <param argument="--no-scaffold-ec" type="boolean" label="Skip assembly/scaffolding error check each round" truevalue="--no-scaffold-ec" falsevalue="" help="Will also prevent any break.agp output files"/>
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110 </when>
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111 <when value="agp_to_fasta">
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112 <param name="agp" type="data" format="agp" label="Input AGP file"/>
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113 <param name="fasta" type="data" format="fasta" label="Contig fasta file"/>
5
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114 <param name="length" type="integer" label="Output fasta line length" value="60" min="1"/>
0
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115 </when>
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116 </conditional>
2
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117 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
0
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118 </inputs>
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119 <outputs>
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120 <!-- INITIAL ROUNDS -->
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121 <collection name="initial_agp_break" type="list" label="${tool.name} on ${on_string}: AGP initial break files">
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122 <filter>function['function_select'] == "yahs"</filter>
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123 <discover_datasets pattern="__name_and_ext__" directory="initial_break" ext="agp"/>
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124 </collection>
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125 <collection name="agp_break" type="list" label="${tool.name} on ${on_string}: AGP break files">
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126 <filter> function['function_select'] == "yahs"</filter>
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127 <discover_datasets pattern="__name_and_ext__" directory="agp_break" ext="agp"/>
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128 </collection>
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129 <collection name="agp_out" type="list" label="${tool.name} on ${on_string}: AGP scaffolding results files">
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130 <filter>function['function_select'] == "yahs"</filter>
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131 <discover_datasets pattern="__name_and_ext__" directory="agp_out" ext="agp"/>
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132 </collection>
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133 <!-- FINAL FILES -->
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134 <data format="agp" name="final_agp_out" label="${tool.name} on ${on_string}: Final scaffolds agp output" from_work_dir="final_outs/yahs_out_scaffolds_final.agp">
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135 <filter>function['function_select'] == "yahs"</filter>
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136 </data>
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137 <data format="fasta" name="final_fasta_out" label="${tool.name} on ${on_string}: Final scaffolds fasta output" from_work_dir="final_outs/yahs_out_scaffolds_final.fa">
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138 <filter>function['function_select'] == "yahs"</filter>
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139 </data>
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140 <data format="fasta" name="fasta_from_agp" label="${tool.name} on ${on_string}: agp to fasta" from_work_dir="output.fasta">
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141 <filter>function['function_select'] == "agp_to_fasta"</filter>
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142 </data>
2
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143 <data format="txt" name="log_file" from_work_dir="output.log" label="${tool.name} ${on_string}, log file">
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144 <filter>log_out</filter>
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145 </data>
0
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146 </outputs>
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147 <tests>
3
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148 <!-- TEST 1 -->
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149 <test expect_num_outputs="5">
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150 <conditional name="function">
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151 <param name="function_select" value="yahs"/>
5
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152 <param name="fasta" value="test.fasta" ftype="fasta"/>
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153 <param name="bfile" value="test.bed" ftype="bed" />
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154 <param name="agp" value="test.agp" ftype="agp"/>
0
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155 <param name="res" value="50000,100000,150000,2000000,1000000"/>
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156 </conditional>
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157 <output name="final_agp_out" file="test_01_scaffolds_final.agp" ftype="agp"/>
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158 <output name="final_fasta_out" file="test_01_scaffolds_final.fa" ftype="fasta"/>
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159 <!-- COMMAND: yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 -->
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160 </test>
3
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161 <!-- TEST 2 -->
0
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162 <test expect_num_outputs="5">
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163 <conditional name="function">
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164 <param name="function_select" value="yahs"/>
5
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165 <param name="fasta" value="test.fasta" ftype="fasta"/>
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166 <param name="bfile" value="test.bed" ftype="bed"/>
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167 <param name="no_contig_ec" value="true"/>
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168 <param name="no_scaffold_ec" value="true"/>
0
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169 </conditional>
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170 <output name="final_agp_out" file="test_02_scaffolds_final.agp" ftype="agp"/>
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171 <output name="final_fasta_out" file="test_02_scaffolds_final.fa" ftype="fasta"/>
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172 <output_collection name="agp_break">
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173 <element name="yahs_out_no_break" file="test_02_no_break.agp" ftype="agp"/>
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174 </output_collection>
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175 <!-- COMMAND: yahs test.fasta test.bed -\-no-contig-ec -\-no-scaffold-ec -o test_2 -->
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176 </test>
3
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177 <!-- TEST 3 -->
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178 <test expect_num_outputs="6">
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179 <conditional name="function">
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180 <param name="function_select" value="yahs"/>
5
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181 <param name="fasta" value="test2.fasta" ftype="fasta"/>
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182 <param name="bfile" value="test2.bam" ftype="bam"/>
3
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183 <param name="res" value="1000,2000,5000,10000,20000,50000,100000,200000,500000"/>
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184 <conditional name="enzyme_conditional">
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185 <param name="enzyme_options" value="not_specified"/>
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186 </conditional>
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187 </conditional>
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188 <param name="log_out" value="yes"/>
5
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189 <output name="log_file" ftype="txt">
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190 <assert_contents>
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191 <has_text text="[I::dump_links_from_bam_file] dumped 6399 read pairs from 17675 records: 6297 intra links + 102 inter links"/>
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192 </assert_contents>
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193 </output>
3
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194 <!-- COMMAND: yahs test.fasta test.bam -r 1000,2000,5000,10000,20000,50000,100000,200000,500000 -o test_3 -->
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195 </test>
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196 <!-- TEST 4 -->
0
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197 <test expect_num_outputs="5">
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198 <conditional name="function">
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199 <param name="function_select" value="yahs"/>
5
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200 <param name="fasta" value="test2.fasta" ftype="fasta"/>
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201 <param name="bfile" value="test2.bed" ftype="bed"/>
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202 <param name="quality" value="10"/>
0
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203 <param name="length" value="20"/>
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204 <conditional name="enzyme_conditional">
3
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205 <param name="enzyme_options" value="not_specified"/>
0
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206 </conditional>
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207 </conditional>
3
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208 <output name="final_agp_out" file="test_04_scaffolds_final.agp" ftype="agp"/>
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209 <output name="final_fasta_out" file="test_04_scaffolds_final.fa" ftype="fasta"/>
0
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210 <output_collection name="initial_agp_break">
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211 <element name="yahs_out_inital_break_01" file="test_04_initial_break.agp" ftype="agp"/>
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212 </output_collection>
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213 </test>
3
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214 <!-- TEST 5 -->
0
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215 <test expect_num_outputs="1">
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216 <conditional name="function">
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217 <param name="function_select" value="agp_to_fasta"/>
5
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218 <param name="fasta" value="test.fasta" ftype="fasta"/>
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219 <param name="agp" value="test.agp" ftype="agp"/>
0
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220 <param name="length" value="20"/>
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221 </conditional>
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222 <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/>
2
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223 <!-- COMMAND: agp_to_fasta test.fasta test.agp -l 20 -o test_4 -->
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224 </test>
3
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225 <!-- TEST 6 -->
2
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226 <test expect_num_outputs="6">
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227 <conditional name="function">
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228 <param name="function_select" value="yahs"/>
5
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229 <param name="fasta" value="test.fasta" ftype="fasta"/>
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230 <param name="bfile" value="test.bed" ftype="bed"/>
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231 <param name="agp" value="test.agp" ftype="agp"/>
2
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232 <param name="res" value="50000,100000,150000,2000000,1000000"/>
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233 </conditional>
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234 <param name="log_out" value="yes"/>
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235 <output name="final_agp_out" file="test_01_scaffolds_final.agp" ftype="agp"/>
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236 <output name="final_fasta_out" file="test_01_scaffolds_final.fa" ftype="fasta"/>
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237 <output name="log_file" ftype="txt">
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238 <assert_contents>
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239 <has_text text="[I::main] CMD: yahs"/>
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240 </assert_contents>
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241 </output>
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242 <!-- COMMAND: yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 -->
0
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243 </test>
4
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244 <!-- TEST 7: omnic prep -->
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245 <test expect_num_outputs="6">
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246 <conditional name="function">
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247 <param name="function_select" value="yahs"/>
5
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248 <param name="fasta" value="test.fasta" ftype="fasta"/>
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249 <param name="bfile" value="test.bed" ftype="bed"/>
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250 <conditional name="enzyme_conditional">
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251 <param name="enzyme_options" value="preconfigured"/>
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252 <param name="preconfigured_enzymes" value="omnic"/>
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253 </conditional>
4
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254 </conditional>
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255 <param name="log_out" value="yes"/>
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256 <output name="log_file" ftype="txt">
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257 <assert_contents>
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258 <not_has_text text="-e"/>
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259 </assert_contents>
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260 </output>
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261 </test>
5
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262 <!-- TEST 8: qname_sorted-->
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263 <test expect_num_outputs="6">
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264 <conditional name="function">
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265 <param name="function_select" value="yahs"/>
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266 <param name="fasta" value="test2.fasta" ftype="fasta"/>
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267 <param name="bfile" value="test3.qname_sorted.bam" ftype="qname_sorted.bam"/>
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268 <param name="res" value="1000,2000,5000,10000,20000,50000,100000,200000,500000"/>
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269 <conditional name="enzyme_conditional">
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270 <param name="enzyme_options" value="not_specified"/>
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271 </conditional>
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272 </conditional>
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273 <param name="log_out" value="yes"/>
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274 <output name="log_file" ftype="txt">
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275 <assert_contents>
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276 <has_text text="[I::dump_links_from_bam_file] dumped 6399 read pairs from 17675 records: 6399 intra links + 0 inter links"/>
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277 </assert_contents>
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278 </output>
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279 </test>
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280 <!-- TEST 9: unsorted-->
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281 <test expect_num_outputs="6">
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282 <conditional name="function">
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283 <param name="function_select" value="yahs"/>
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284 <param name="fasta" value="test2.fasta" ftype="fasta"/>
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285 <param name="bfile" value="test2.unsorted.bam" ftype="bam"/>
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286 <param name="res" value="1000,2000,5000,10000,20000,50000,100000,200000,500000"/>
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287 <conditional name="enzyme_conditional">
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288 <param name="enzyme_options" value="not_specified"/>
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289 </conditional>
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290 </conditional>
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291 <param name="log_out" value="yes"/>
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292 <output name="log_file" ftype="txt">
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293 <assert_contents>
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294 <has_text text="[I::dump_links_from_bam_file] dumped 6399 read pairs from 17675 records: 6297 intra links + 102 inter links"/>
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295 </assert_contents>
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296 </output>
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297 <!-- COMMAND: yahs test.fasta test.bam -r 1000,2000,5000,10000,20000,50000,100000,200000,500000 -o test_3 -->
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298 </test>
0
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299 </tests>
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300 <help><![CDATA[
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301 YaHS is scaffolding tool using Hi-C data. It relies on a new algorithm for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. YaHS has been tested in a wide range of genome assemblies. Compared to other Hi-C scaffolding tools, it usually generates more contiguous scaffolds - especially with a higher N90 and L90 statistics. It is also super fast - takes less than 5 minutes to reconstruct the human genome from an assembly of 5,483 contigs with ~45X Hi-C data.
0
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302 ]]></help>
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303 <citations>
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304 <citation type="doi">10.5281/zenodo.5848772</citation>
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305 </citations>
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306 </tool>