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annotate yahs.xml @ 4:425e63adcc5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit be65e1846c9d4d63e80c01625e6e5f0d613948fe
author iuc
date Thu, 09 Mar 2023 21:59:34 +0000
parents 39495e107274
children ff4031bfaa22
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d87433f2a54d 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">
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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>
4
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5 <token name="@VERSION_SUFFIX@">1</token>
0
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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>
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10 <requirement type="package" version="3.9">python</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 #if $function.function_select == "yahs":
d87433f2a54d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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14 ln -s '$function.fasta' input.fasta &&
d87433f2a54d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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15 #if $function.bfile.ext == "bam":
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16 ln -s '$function.bfile' input.bam &&
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17 #else if $function.bfile.ext == "bed":
d87433f2a54d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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18 ln -s '$function.bfile' input.bed &&
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19 #end if
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20 #if $function.agp:
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21 ln -s '$function.agp' input.agp &&
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22 #end if
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23 samtools faidx input.fasta &&
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24 mkdir initial_break agp_out agp_break final_outs &&
3
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25 yahs --no-mem-check input.fasta
0
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26 #if $function.bfile.ext == "bam":
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27 input.bam
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28 #else if $function.bfile.ext == "bed":
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29 input.bed
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30 #end if
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31 #if $agp:
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32 -a input.agp
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33 #end if
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34 #if $function.res:
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35 -r $function.res
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36 #end if
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37 #if $function.enzyme_conditional.enzyme_options == 'preconfigured':
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38 #if $function.enzyme_conditional.preconfigured_enzymes == 'dovetail'
d87433f2a54d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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39 -e 'GATC'
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40 #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima1'
d87433f2a54d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 92823b21835509dde34557b6922e1b9a39311069
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41 -e 'GATC,GANTC'
4
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42 #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima2'
0
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43 -e 'GATC,GANTC,CTNAG,TTAA'
4
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44 #else if $function.enzyme_conditional.preconfigured_enzymes == 'omnic'
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45
0
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46 #end if
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47 #else if $function.enzyme_conditional.enzyme_options == 'specific':
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48 -e '${function.enzyme_conditional.manual_enzyme}'
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49 #end if
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50 #if $function.length:
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51 -l $function.length
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52 #end if
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53 #if $function.quality:
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54 -q $function.quality
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55 #end if
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56 $function.no_contig_ec
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57 $function.no_scaffold_ec
2
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58 -o yahs_out
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59 #if $log_out
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60 2> output.log
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61 #end if
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62 && ls -lah &&
0
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63 python '$__tool_directory__/move_files.py'
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64 && ls -lah ./*
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65 #else:
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66 ln -s '$function.fasta' input.fasta &&
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67 ln -s '$function.agp' input.agp &&
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68 agp_to_fasta input.agp input.fasta
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69 #if $function.length:
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70 -l $function.length
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71 #end if
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72 -o output.fasta
2
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73 #if $log_out:
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74 2> output.log
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75 #end if
0
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76 #end if
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77 ]]></command>
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78 <inputs>
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79 <conditional name="function">
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80 <param name="function_select" type="select" label="Which function would you like to run?">
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81 <option value="yahs">YAHS</option>
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82 <option value="agp_to_fasta">AGP to fasta</option>
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83 </param>
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84 <when value="yahs">
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85 <param name="fasta" type="data" format="fasta" label="Input contig sequences"/>
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86 <param name="bfile" type="data" format="bam,bed" label="Alignment file of Hi-C reads to contigs"/>
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87 <param name="agp" argument="-a" type="data" format="agp" optional="true" label="Input AGP file (for rescaffolding)"
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88 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"/>
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89 <param name="res" argument="-r" type="text" label="Resolutions" optional="true"
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90 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"/>
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91 <conditional name="enzyme_conditional">
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92 <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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93 The enzyme frequency in contigs is used to normalize the Hi-C interaction frequency. Note that you need to specify the actual
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94 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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95 use an enzyme-free prep, e.g. Omin-C.">
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96 <option value="not_specified">Not specified</option>
0
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97 <option value="preconfigured">Preconfigured restriction enzymes</option>
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98 <option value="specific">Enter a specific sequence</option>
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99 </param>
2
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100 <when value="not_specified"/>
0
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101 <when value="preconfigured">
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102 <param name="preconfigured_enzymes" argument="-e" type="select" label="Preconfigured enzymes">
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103 <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option>
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104 <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option>
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105 <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option>
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106 <option value="omnic">Dovetail Omni-C: enzyme-free prep</option>
0
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107 </param>
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108 </when>
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109 <when value="specific">
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110 <param name="manual_enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)"
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111 help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT').">
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112 <validator type="expression" message="Only alphabetical letters and the comma can be used in to define restriction enzym sequences.">value.replace(',', '').isalpha()</validator>
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113 </param>
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114 </when>
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115 </conditional>
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116 <param name="length" argument="-l" type="integer" label="Minimum contig length included for scaffolding" min="1" optional="true"/>
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117 <param name="quality" argument="-q" type="integer" label="Minimum read mapping quality (for BAM input only)" min="1" optional="true"/>
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118 <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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119 <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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120 </when>
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121 <when value="agp_to_fasta">
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122 <param name="agp" type="data" format="agp" label="Input AGP file"/>
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123 <param name="fasta" type="data" format="fasta" label="Contig fasta file"/>
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124 <param name="length" type='integer' label="Output fasta line length" value="60" min="1"/>
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125 </when>
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126 </conditional>
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127 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
0
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128 </inputs>
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129 <outputs>
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130 <!-- INITIAL ROUNDS -->
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131 <collection name="initial_agp_break" type="list" label="${tool.name} on ${on_string}: AGP initial break files">
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132 <filter>function['function_select'] == "yahs"</filter>
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133 <discover_datasets pattern="__name_and_ext__" directory="initial_break" ext="agp"/>
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134 </collection>
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135 <collection name="agp_break" type="list" label="${tool.name} on ${on_string}: AGP break files">
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136 <filter> function['function_select'] == "yahs"</filter>
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137 <discover_datasets pattern="__name_and_ext__" directory="agp_break" ext="agp"/>
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138 </collection>
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139 <collection name="agp_out" type="list" label="${tool.name} on ${on_string}: AGP scaffolding results files">
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140 <filter>function['function_select'] == "yahs"</filter>
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141 <discover_datasets pattern="__name_and_ext__" directory="agp_out" ext="agp"/>
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142 </collection>
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143 <!-- FINAL FILES -->
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144 <data format="agp" name="final_agp_out" label="${tool.name} on ${on_string}: Final scaffolds agp output" from_work_dir="final_outs/yahs_out_scaffolds_final.agp">
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145 <filter>function['function_select'] == "yahs"</filter>
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146 </data>
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147 <data format="fasta" name="final_fasta_out" label="${tool.name} on ${on_string}: Final scaffolds fasta output" from_work_dir="final_outs/yahs_out_scaffolds_final.fa">
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148 <filter>function['function_select'] == "yahs"</filter>
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149 </data>
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150 <data format="fasta" name="fasta_from_agp" label="${tool.name} on ${on_string}: agp to fasta" from_work_dir="output.fasta">
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151 <filter>function['function_select'] == "agp_to_fasta"</filter>
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152 </data>
2
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153 <data format="txt" name="log_file" from_work_dir="output.log" label="${tool.name} ${on_string}, log file">
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154 <filter>log_out</filter>
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155 </data>
0
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156 </outputs>
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157 <tests>
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158 <!-- TEST 1 -->
0
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159 <test expect_num_outputs="5">
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160 <conditional name="function">
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161 <param name="function_select" value="yahs"/>
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162 <param name="fasta" value="test.fasta"/>
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163 <param name="bfile" value="test.bed"/>
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164 <param name="agp" value="test.agp"/>
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165 <param name="res" value="50000,100000,150000,2000000,1000000"/>
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166 </conditional>
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167 <output name="final_agp_out" file="test_01_scaffolds_final.agp" ftype="agp"/>
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168 <output name="final_fasta_out" file="test_01_scaffolds_final.fa" ftype="fasta"/>
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169 <!-- COMMAND: yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 -->
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170 </test>
3
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171 <!-- TEST 2 -->
0
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172 <test expect_num_outputs="5">
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173 <conditional name="function">
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174 <param name="function_select" value="yahs"/>
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175 <param name="fasta" value="test.fasta"/>
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176 <param name="bfile" value="test.bed"/>
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177 <param name="no_contig_ec" value="--no-contig-ec"/>
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178 <param name="no_scaffold_ec" value="--no-scaffold-ec"/>
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179 </conditional>
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180 <output name="final_agp_out" file="test_02_scaffolds_final.agp" ftype="agp"/>
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181 <output name="final_fasta_out" file="test_02_scaffolds_final.fa" ftype="fasta"/>
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182 <output_collection name="agp_break">
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183 <element name="yahs_out_no_break" file="test_02_no_break.agp" ftype="agp"/>
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184 </output_collection>
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185 <!-- COMMAND: yahs test.fasta test.bed -\-no-contig-ec -\-no-scaffold-ec -o test_2 -->
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186 </test>
3
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187 <!-- TEST 3 -->
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188 <test expect_num_outputs="6">
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189 <conditional name="function">
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190 <param name="function_select" value="yahs"/>
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191 <param name="fasta" value="test2.fasta"/>
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192 <param name="bfile" value="test2.bam"/>
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193 <param name="res" value="1000,2000,5000,10000,20000,50000,100000,200000,500000"/>
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194 <conditional name="enzyme_conditional">
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195 <param name="enzyme_options" value="not_specified"/>
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196 </conditional>
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197 </conditional>
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198 <param name="log_out" value="yes"/>
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199 <output name="log_file" ftype="txt">
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200 <assert_contents>
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201 <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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202 </assert_contents>
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203 </output>
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204 <!-- COMMAND: yahs test.fasta test.bam -r 1000,2000,5000,10000,20000,50000,100000,200000,500000 -o test_3 -->
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205 </test>
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206 <!-- TEST 4 -->
0
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207 <test expect_num_outputs="5">
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208 <conditional name="function">
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209 <param name="function_select" value="yahs"/>
3
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210 <param name="fasta" value="test2.fasta"/>
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211 <param name="bfile" value="test2.bed"/>
0
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212 <param name="qual" value="10"/>
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213 <param name="length" value="20"/>
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214 <conditional name="enzyme_conditional">
3
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215 <param name="enzyme_options" value="not_specified"/>
0
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216 </conditional>
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217 </conditional>
3
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218 <output name="final_agp_out" file="test_04_scaffolds_final.agp" ftype="agp"/>
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219 <output name="final_fasta_out" file="test_04_scaffolds_final.fa" ftype="fasta"/>
0
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220 <output_collection name="initial_agp_break">
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221 <element name="yahs_out_inital_break_01" file="test_04_initial_break.agp" ftype="agp"/>
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222 </output_collection>
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223 </test>
3
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224 <!-- TEST 5 -->
0
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225 <test expect_num_outputs="1">
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226 <conditional name="function">
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227 <param name="function_select" value="agp_to_fasta"/>
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228 <param name="fasta" value="test.fasta"/>
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229 <param name="agp" value="test.agp"/>
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230 <param name="length" value="20"/>
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231 </conditional>
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232 <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/>
2
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233 <!-- COMMAND: agp_to_fasta test.fasta test.agp -l 20 -o test_4 -->
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234 </test>
3
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235 <!-- TEST 6 -->
2
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236 <test expect_num_outputs="6">
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237 <conditional name="function">
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238 <param name="function_select" value="yahs"/>
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239 <param name="fasta" value="test.fasta"/>
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240 <param name="bfile" value="test.bed"/>
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241 <param name="agp" value="test.agp"/>
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242 <param name="res" value="50000,100000,150000,2000000,1000000"/>
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243 </conditional>
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244 <param name="log_out" value="yes"/>
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245 <output name="final_agp_out" file="test_01_scaffolds_final.agp" ftype="agp"/>
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246 <output name="final_fasta_out" file="test_01_scaffolds_final.fa" ftype="fasta"/>
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247 <output name="log_file" ftype="txt">
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248 <assert_contents>
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249 <has_text text="[I::main] CMD: yahs"/>
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250 </assert_contents>
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251 </output>
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252 <!-- COMMAND: yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 -->
0
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253 </test>
4
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254 <!-- TEST 7: omnic prep -->
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255 <test expect_num_outputs="6">
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256 <conditional name="function">
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257 <param name="function_select" value="yahs"/>
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258 <param name="fasta" value="test.fasta"/>
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259 <param name="bfile" value="test.bed"/>
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260 </conditional>
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261 <conditional name="enzyme_conditional">
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262 <param name="enzyme_options" value="preconfigured"/>
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263 <param name="preconfigured_enzymes" value="omnic"/>
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264 </conditional>
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265 <param name="log_out" value="yes"/>
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266 <output name="log_file" ftype="txt">
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267 <assert_contents>
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268 <not_has_text text="-e"/>
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269 </assert_contents>
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270 </output>
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271 </test>
0
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272 </tests>
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273 <help><![CDATA[
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274 YaHS is scaffolding tool using Hi-C data. It relies on a new algothrim 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.
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275 ]]></help>
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276 <citations>
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277 <citation type="doi">10.5281/zenodo.5848772</citation>
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278 </citations>
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279 </tool>