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annotate mitohifi.xml @ 0:7c5e8ee8c0a7 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
author bgruening
date Sat, 29 May 2021 12:49:57 +0000
parents
children cc15449dc2bb
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0
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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1 <tool id='mitohifi' name='MitoHiFi' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'>
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2 <description>assembly mitogenomes from Pacbio HiFi reads</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='edam_ontology' />
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7 <expand macro='requirements' />
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8 <command detect_errors='exit_code'><![CDATA[
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9 #if $operation_mode.command == 'find_reference'
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10 findMitoReference.py
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11 --species '${operation_mode.species}'
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12 --email '${operation_mode.email}'
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13 --outfolder ./
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14 #if $operation_mode.min_length
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15 --min_length $operation_mode.min_length
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16 #end if
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17 $operation_mode.exact_specie
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18 && mv ./*fasta ./reference_genome.fasta
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19 && mv ./*gb ./reference_genome.gb
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20 #elif $operation_mode.command == 'mitohifi'
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21 ln -s '${operation_mode.reference_genbank}' related_mito.gb
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22 && ln -s '${operation_mode.reference_fasta}' related_mito.fasta
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23
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24 && mitohifi_v2.py
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25 #if $operation_mode.input_option.input == 'pacbio'
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26 -r '${ ' '.join(["%s" % $x for $x in $operation_mode.input_option.input_reads]) }'
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27 -m $operation_mode.input_option.bloom_filter
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28 #else
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29 -c '${operation_mode.input_option.input_assembly}'
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30 #end if
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31 -f related_mito.fasta
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32 -g related_mito.gb
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33 #if $operation_mode.advanced_options.query_blast
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34 -p $operation_mode.advanced_options.query_blast
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35 #end if
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36 #if $operation_mode.advanced_options.circular_size
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37 --circular-size $operation_mode.advanced_options.circular_size
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38 #end if
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39 #if $operation_mode.advanced_options.circular_offset
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40 --circular-offset $operation_mode.advanced_options.circular_offset
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41 #end if
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42 -o $operation_mode.genetic_code
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43 -t \${GALAXY_SLOTS:-1}
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44 #if $operation_mode.output_zip
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45 && zip -r output.zip contigs_* final_mitogenome* reads_mapping_and_assembly/
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46 #end if
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47 #end if
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48 ]]> </command>
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49 <inputs>
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50 <conditional name="operation_mode">
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51 <param name="command" type="select" label="Operation type selector" help="Select a type of operation">
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52 <option value="find_reference">Find a close-related mitochondrial reference genome</option>
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53 <option value="mitohifi">Run MitoHiFi</option>
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54 </param>
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55 <when value="find_reference">
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56 <param argument="--species" type="text" value="" label="Specie name" help="Specie name in binomial nomenclature">
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57 <sanitizer invalid_char="">
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58 <valid initial="string.letters,string.digits">
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59 <add value=" "/>
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60 </valid>
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61 </sanitizer>
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62 </param>
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63 <param argument="--email" type="text" value="" label="Email" help="Required for NCBI database query">
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64 <sanitizer invalid_char="">
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65 <valid initial="string.letters,string.digits">
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66 <add value="@"/>
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67 <add value="."/>
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68 <add value="_"/>
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69 <add value=" "/>
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70 </valid>
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71 </sanitizer>
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72 </param>
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73 <param argument="--min_length" type="integer"
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74 min="0" max="15000000" value="" optional="True" label="Minimal appropriate length" />
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75 <param name="exact_specie" argument="-s" type="boolean"
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76 truevalue="-s" falsevalue="" checked="False" optional="True" label="Search for an exact species"/>
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77 </when>
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78 <when value="mitohifi">
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79 <conditional name="input_option">
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80 <param name="input" type="select" label="Input mode">
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81 <option value="pacbio">Pacbio Hifi Reads</option>
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82 <option value="assembly">Assembled contigs/scaffolds</option>
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83 </param>
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84 <when value="pacbio">
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85 <param name="input_reads" argument="-r" type="data"
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86 format="fasta,fasta.gz,fastq,fastq.gz" multiple="True" label="Pacbio Hifi reads"
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87 help="The reads are mapped to close-related species (to pull out mito-reads and exclude possible NUMTS) and assembled by using Hifiasm"/>
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88 <param name="bloom_filter" argument="-m" type="integer" min="0" max="39" value="0" label="Number of bits for bloom filter" help="For small genomes, use -f0 to disable the initial bloom filter which takes 16GB memory at the beginning. For genomes much larger than human, applying -f38 or even -f39 is preferred to save memory on k-mer counting."/>
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89 </when>
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90 <when value="assembly">
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91 <param name="input_assembly" argument="-c" type="data"
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92 format="fasta" label="Assembled contigs/scaffolds"
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93 help="Assembled contigs/scaffolds in FASTA format will be used to find the mitogenome"/>
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94 </when>
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95 </conditional>
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96 <param name="reference_fasta" argument="-f" type="data"
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97 format="fasta,fasta.gz" multiple="True" label="Close-related mitogenome in fasta format"
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98 help="Close-related mitogenome is fasta format"/>
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99 <param name="reference_genbank" argument="-g" type="data"
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100 format="genbank,genbank.gz" multiple="True" optional="True" label="Close-related mitogenome in genbank format"
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101 help="Close-related mitogenome is genbank format"/>
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102 <param name="genetic_code" type="select" label="Genetic code" help="Organism genetic code following NCBI table (for mitogenome annotation)">
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103 <option value="1">Standard code</option>
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104 <option value="2">Vertebrate mitochondrial code</option>
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105 <option value="3">Yeast mitochondrial code</option>
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106 <option value="4">Mold, Protozoan and Coelenterate mitochondrial code and the Mycoplasma/Spiroplasma code </option>
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107 <option value="5">Invertebrate mitochondrial code </option>
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108 <option value="6">Ciliate, Dasycladacean and Hexamita nuclear code</option>
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109 <option value="9">Echinoderm and Flatworm mitochondrial code</option>
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110 <option value="10">Euplotid nuclear code</option>
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111 <option value="11">Bacterial, Archaeal and plant plastid code</option>
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112 <option value="12">Alternative yeast nuclear code</option>
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113 <option value="13">Ascidian mitochondrial code</option>
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114 <option value="14">Alternative flatworm mitochondrial code</option>
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115 <option value="16">Chlorophycean mitochondrial code</option>
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116 <option value="21">Trematode mitochondrial code</option>
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117 <option value="22">Scenedesmus obliquus mitochondrial code</option>
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118 <option value="23">Thraustochytrium mitochondrial code</option>
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119 <option value="24">Pterobranchia mitochondrial code</option>
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120 <option value="25">Candidate Division SR1 and Gracilibacteria code</option>
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121 </param>
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122 <section name="advanced_options" title="Advanced options">
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123 <param name="query_blast" argument="-p" type="integer"
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124 min="0" max="100" value="" optional="True" label="Blast percentage identity"
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125 help="Percentage of query in the blast match with close-related mito. By default it is going to chose any contig which has 50% or more of its length in the blast match." />
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126 <param argument="--circular-size" type="integer"
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127 min="0" max="15000000" value="" optional="True" label="Estimated mtDNA size"
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128 help="Size to consider when checking for circularization" />
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129 <param argument="--circular_offset" type="integer"
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130 min="0" max="5000" value="" optional="True" label="Circularization offset"
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131 help="Offset from start and finish to consider when looking for circularization" />
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132 <param name="outputs" type="select" label="Optional outputs" multiple="True" display="checkboxes">
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133 <option value="contigs_filtering">Contigs filtering</option>
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134 <option value="contigs_circularization">Contigs circularization</option>
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135 <option value="potential_contigs">Potential contigs</option>
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136 <option value="final_mitogenome_alignment">Final mitogenome alignment</option>
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137 </param>
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138 </section>
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139 <param name="output_zip" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate an output package in ZIP format" help="This option creates a zip file with all the files and folders generated by MitoHiFi." />
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140 </when>
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141 </conditional>
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142 </inputs>
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143 <outputs>
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144 <data name="fasta_reference" format="fasta" from_work_dir="reference_genome.fasta" label="${tool.name} on ${on_string}: reference genome (FASTA)">
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145 <filter> operation_mode['command'] == 'find_reference'</filter>
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146 </data>
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147 <data name="genbank_reference" format="genbank" from_work_dir="reference_genome.gb" label="${tool.name} on ${on_string}: reference genome (genbank)">
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148 <filter> operation_mode['command'] == 'find_reference'</filter>
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149 </data>
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150 <data name="mitogenome_fasta" format="fasta" from_work_dir="final_mitogenome.fasta" label="${tool.name} on ${on_string}: final mitogenome (FASTA)">
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151 <filter> operation_mode['command'] == 'mitohifi'</filter>
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152 </data>
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153 <data name="mitogenome_genbank" format="genbank" from_work_dir="final_mitogenome.gb" label="${tool.name} on ${on_string}: final mitogenome (genbank)">
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154 <filter> operation_mode['command'] == 'mitohifi'</filter>
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155 </data>
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156 <data name="parsed_blast" format="txt" from_work_dir="contigs_filtering/parsed_blast.txt" label="${tool.name} on ${on_string}: parsed BLAST">
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157 <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_filtering' in operation_mode['advanced_options']['outputs'])</filter>
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158 </data>
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159 <data name="parsed_blast_all" format="txt" from_work_dir="contigs_filtering/parsed_blast_all.txt" label="${tool.name} on ${on_string}: parsed BLAST (all)">
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160 <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_filtering' in operation_mode['advanced_options']['outputs'])</filter>
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161 </data>
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162 <data name="contigs_ids" format="txt" from_work_dir="contigs_filtering/contigs_ids.txt" label="${tool.name} on ${on_string}: contigs IDS">
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163 <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_filtering' in operation_mode['advanced_options']['outputs'])</filter>
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164 </data>
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165 <data name="contigs_circularization" format="txt" from_work_dir="contigs_circularization/all_contigs.circularisationCheck.txt" label="${tool.name} on ${on_string}: contigs circularization">
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166 <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_circularization' in operation_mode['advanced_options']['outputs'])</filter>
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167 </data>
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168 <collection name="potential_contigs" type='list' label='${tool.name} on ${on_string}: potential contigs'>
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169 <discover_datasets pattern='__designation_and_ext__' format='txt' directory='potential_contigs' />
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170 <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'potential_contigs' in operation_mode['advanced_options']['outputs'])</filter>
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171 </collection>
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172 <data name="final_mitogenome" format="fasta" from_work_dir="final_mitogenome_choice/all_mitogenomes.rotated.aligned.fa" label="${tool.name} on ${on_string}: mitogenomes alignment">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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173 <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'final_mitogenome_alignment' in operation_mode['advanced_options']['outputs'])</filter>
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174 </data>
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175 <data name="hifiasm" format="fasta" from_work_dir="reads_mapping_and_assembly/gbk.HiFiMapped.bam.fasta" label="${tool.name} on ${on_string}: reads mapped to close-related mtDNA">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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176 <filter>operation_mode['command'] == 'mitohifi' and operation_mode['input_option']['input'] == 'pacbio'</filter>
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177 </data>
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178 <data name="hifiasm_filtered" format="fasta" from_work_dir="reads_mapping_and_assembly/gbk.HiFiMapped.bam.filtered.fasta" label="${tool.name} on ${on_string}: mapped reads filtered by size">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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179 <filter>operation_mode['command'] == 'mitohifi' and operation_mode['input_option']['input'] == 'pacbio'</filter>
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180 </data>
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181 <data name="hifiasm_contigs" format="fasta" from_work_dir="reads_mapping_and_assembly/hifiasm.contigs.fasta" label="${tool.name} on ${on_string}: Hifiasm contigs">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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182 <filter>operation_mode['command'] == 'mitohifi' and operation_mode['input_option']['input'] == 'pacbio'</filter>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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183 </data>
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184 <data name="zip_file" format="zip" from_work_dir="output.zip" label="${tool.name} on ${on_string}: output files (ZIP)">
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185 <filter>operation_mode['command'] == 'mitohifi' and operation_mode['output_zip']</filter>
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186 </data>
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187 </outputs>
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188 <tests>
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189 <!--Test 01-->
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190 <test expect_num_outputs="2">
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191 <conditional name="operation_mode">
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192 <param name="command" value="find_reference"/>
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193 <param name="species" value="Amphipyra berbera"/>
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194 <param name="email" value="kk16@sanger.ac.uk"/>
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195 <param name="min_length" value="1500"/>
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196 </conditional>
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197 <output name="fasta_reference" ftype="fasta">
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198 <assert_contents>
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199 <has_size value="15742"/>
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200 <has_line line=">NC_054179.1 Spodoptera exempta mitochondrion, complete genome"/>
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201 </assert_contents>
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202 </output>
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203 <output name="genbank_reference" ftype="genbank">
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204 <assert_contents>
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205 <has_size value="43468"/>
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206 <has_line line="DEFINITION Spodoptera exempta mitochondrion, complete genome."/>
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207 </assert_contents>
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208 </output>
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209 </test>
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210 <!--Test 02-->
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211 <test expect_num_outputs="5">
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212 <conditional name="operation_mode">
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213 <param name="command" value="mitohifi"/>
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214 <conditional name="input_option">
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215 <param name="input" value="pacbio"/>
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216 <param name="input_reads" value="pacbio_01.fasta.gz"/>
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217 </conditional>
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218 <param name="reference_fasta" value="related_mitogenome.fasta"/>
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219 <param name="reference_genbank" value="related_mitogenome.gb"/>
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220 <param name="genetic_code" value="5"/>
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221 </conditional>
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222 <output name="mitogenome_fasta" ftype="fasta">
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223 <assert_contents>
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224 <has_size value="15337"/>
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225 <has_line line=">ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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226 </assert_contents>
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227 </output>
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228 <output name="mitogenome_genbank" ftype="genbank">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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229 <assert_contents>
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230 <has_size value="30637"/>
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231 <has_line line="DEFINITION ptg000001c_rotated"/>
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232 </assert_contents>
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233 </output>
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234 <output name="hifiasm" ftype="fasta">
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235 <assert_contents>
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236 <has_size value="2063025"/>
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237 <has_line line=">m64094_200908_163909/67999/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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238 </assert_contents>
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239 </output>
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240 <output name="hifiasm_filtered" ftype="fasta">
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241 <assert_contents>
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242 <has_size value="2097153"/>
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243 <has_line line=">m64094_200908_163909/1605/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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244 </assert_contents>
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245 </output>
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246 <output name="hifiasm_contigs" ftype="fasta">
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247 <assert_contents>
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248 <has_size value="15329"/>
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249 <has_line line=">ptg000001c"/>
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250 </assert_contents>
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251 </output>
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252 </test>
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253 <!--Test 03-->
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diff changeset
254 <test expect_num_outputs="5">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
255 <conditional name="operation_mode">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
256 <param name="command" value="mitohifi"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
257 <conditional name="input_option">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
258 <param name="input" value="pacbio"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
259 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
260 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
261 <param name="reference_fasta" value="related_mitogenome.fasta"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
262 <param name="reference_genbank" value="related_mitogenome.gb"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
263 <param name="genetic_code" value="5"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
264 <section name="advanced_options">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
265 <param name="query_blast" value="40"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
266 </section>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
267 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
268 <output name="mitogenome_fasta" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
269 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
270 <has_size value="15337"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
271 <has_line line=">ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
272 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
273 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
274 <output name="mitogenome_genbank" ftype="genbank">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
275 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
276 <has_size value="30637"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
277 <has_line line="DEFINITION ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
278 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
279 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
280 <output name="hifiasm" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
281 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
282 <has_size value="4123737"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
283 <has_line line=">m64094_200908_163909/67999/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
284 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
285 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
286 <output name="hifiasm_filtered" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
287 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
288 <has_size value="4191948"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
289 <has_line line=">m64094_200908_163909/1605/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
290 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
291 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
292 <output name="hifiasm_contigs" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
293 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
294 <has_size value="15329"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
295 <has_line line=">ptg000001c"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
296 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
297 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
298 </test>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
299 <!--Test 04-->
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
300 <test expect_num_outputs="5">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
301 <conditional name="operation_mode">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
302 <param name="command" value="mitohifi"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
303 <conditional name="input_option">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
304 <param name="input" value="pacbio"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
305 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
306 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
307 <param name="reference_fasta" value="related_mitogenome.fasta"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
308 <param name="reference_genbank" value="related_mitogenome.gb"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
309 <param name="genetic_code" value="5"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
310 <section name="advanced_options">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
311 <param name="circular_size" value="120000"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
312 </section>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
313 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
314 <output name="mitogenome_fasta" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
315 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
316 <has_size value="15337"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
317 <has_line line=">ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
318 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
319 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
320 <output name="mitogenome_genbank" ftype="genbank">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
321 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
322 <has_size value="30637"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
323 <has_line line="DEFINITION ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
324 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
325 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
326 <output name="hifiasm" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
327 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
328 <has_size value="4123737"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
329 <has_line line=">m64094_200908_163909/67999/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
330 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
331 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
332 <output name="hifiasm_filtered" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
333 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
334 <has_size value="4191948"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
335 <has_line line=">m64094_200908_163909/1605/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
336 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
337 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
338 <output name="hifiasm_contigs" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
339 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
340 <has_size value="15329"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
341 <has_line line=">ptg000001c"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
342 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
343 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
344 </test>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
345 <!--Test 05-->
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
346 <test expect_num_outputs="5">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
347 <conditional name="operation_mode">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
348 <param name="command" value="mitohifi"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
349 <conditional name="input_option">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
350 <param name='input' value="pacbio"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
351 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
352 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
353 <param name="reference_fasta" value="related_mitogenome.fasta"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
354 <param name="reference_genbank" value="related_mitogenome.gb"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
355 <param name="genetic_code" value="5"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
356 <section name="advanced_options">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
357 <param name="circular_offset" value="20"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
358 </section>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
359 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
360 <output name="mitogenome_fasta" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
361 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
362 <has_size value="15337"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
363 <has_line line=">ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
364 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
365 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
366 <output name="mitogenome_genbank" ftype="genbank">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
367 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
368 <has_size value="30637"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
369 <has_line line="DEFINITION ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
370 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
371 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
372 <output name="hifiasm" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
373 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
374 <has_size value="4123737"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
375 <has_line line=">m64094_200908_163909/67999/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
376 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
377 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
378 <output name="hifiasm_filtered" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
379 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
380 <has_size value="4191948"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
381 <has_line line=">m64094_200908_163909/1605/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
382 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
383 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
384 <output name="hifiasm_contigs" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
385 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
386 <has_size value="15329"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
387 <has_line line=">ptg000001c"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
388 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
389 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
390 </test>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
391 <!--Test 06-->
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
392 <test expect_num_outputs="8">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
393 <conditional name="operation_mode">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
394 <param name="command" value="mitohifi"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
395 <conditional name="input_option">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
396 <param name='input' value="pacbio"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
397 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
398 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
399 <param name="reference_fasta" value="related_mitogenome.fasta"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
400 <param name="reference_genbank" value="related_mitogenome.gb"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
401 <param name="genetic_code" value="5"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
402 <section name="advanced_options">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
403 <param name="outputs" value="contigs_filtering"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
404 </section>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
405 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
406 <output name="mitogenome_fasta" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
407 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
408 <has_size value="15337"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
409 <has_line line=">ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
410 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
411 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
412 <output name="mitogenome_genbank" ftype="genbank">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
413 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
414 <has_size value="30637"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
415 <has_line line="DEFINITION ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
416 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
417 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
418 <output name="hifiasm" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
419 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
420 <has_size value="4123737"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
421 <has_line line=">m64094_200908_163909/67999/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
422 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
423 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
424 <output name="hifiasm_filtered" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
425 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
426 <has_size value="4191948"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
427 <!--<has_line line=">m64094_200908_163909/1605/ccs"/>-->
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
428 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
429 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
430 <output name="hifiasm_contigs" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
431 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
432 <has_size value="15329"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
433 <has_line line=">ptg000001c"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
434 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
435 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
436 <output name="parsed_blast" ftype="txt">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
437 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
438 <has_size value="104"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
439 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
440 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
441 <output name="parsed_blast_all" ftype="txt">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
442 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
443 <has_size value="104"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
444 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
445 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
446 <output name="contigs_ids" ftype="txt">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
447 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
448 <has_size value="11"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
449 <has_line line="ptg000001c"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
450 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
451 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
452 </test>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
453 <!--Test 07-->
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
454 <test expect_num_outputs="6">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
455 <conditional name="operation_mode">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
456 <param name="command" value="mitohifi"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
457 <conditional name="input_option">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
458 <param name="input" value="pacbio"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
459 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
460 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
461 <param name="reference_fasta" value="related_mitogenome.fasta"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
462 <param name="reference_genbank" value="related_mitogenome.gb"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
463 <param name="genetic_code" value="5"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
464 <section name="advanced_options">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
465 <param name="outputs" value="contigs_circularization"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
466 </section>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
467 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
468 <output name="mitogenome_fasta" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
469 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
470 <has_size value="15337"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
471 <has_line line=">ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
472 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
473 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
474 <output name="mitogenome_genbank" ftype="genbank">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
475 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
476 <has_size value="30637"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
477 <has_line line="DEFINITION ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
478 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
479 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
480 <output name="hifiasm" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
481 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
482 <has_size value="4123737"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
483 <has_line line=">m64094_200908_163909/67999/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
484 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
485 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
486 <output name="hifiasm_filtered" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
487 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
488 <has_size value="4191948"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
489 <has_line line=">m64094_200908_163909/1605/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
490 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
491 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
492 <output name="hifiasm_contigs" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
493 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
494 <has_size value="15329"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
495 <has_line line=">ptg000001c"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
496 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
497 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
498 <output name="contigs_circularization" ftype="txt">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
499 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
500 <has_size value="28"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
501 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
502 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
503 </test>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
504 <!--Test 08-->
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
505 <test expect_num_outputs="6">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
506 <conditional name="operation_mode">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
507 <param name="command" value="mitohifi"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
508 <conditional name="input_option">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
509 <param name='input' value="pacbio"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
510 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
511 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
512 <param name="reference_fasta" value="related_mitogenome.fasta"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
513 <param name="reference_genbank" value="related_mitogenome.gb"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
514 <param name="genetic_code" value="5"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
515 <section name="advanced_options">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
516 <param name="outputs" value="contigs_circularization"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
517 </section>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
518 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
519 <output name="mitogenome_fasta" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
520 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
521 <has_size value="15337"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
522 <has_line line=">ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
523 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
524 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
525 <output name="mitogenome_genbank" ftype="genbank">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
526 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
527 <has_size value="30637"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
528 <has_line line="DEFINITION ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
529 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
530 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
531 <output name="hifiasm" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
532 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
533 <has_size value="4123737"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
534 <has_line line=">m64094_200908_163909/67999/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
535 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
536 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
537 <output name="hifiasm_filtered" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
538 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
539 <has_size value="4191948"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
540 <has_line line=">m64094_200908_163909/1605/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
541 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
542 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
543 <output name="hifiasm_contigs" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
544 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
545 <has_size value="15329"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
546 <has_line line=">ptg000001c"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
547 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
548 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
549 <output name="final_mitogenome" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
550 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
551 <has_size value="15329"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
552 <has_line line=">ptg000001c"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
553 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
554 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
555 </test>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
556 <!--Test 09-->
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
557 <test expect_num_outputs="2">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
558 <conditional name="operation_mode">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
559 <param name="command" value="mitohifi"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
560 <conditional name="input_option">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
561 <param name='input' value="assembly"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
562 <param name="input_reads" value="assembly.fa"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
563 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
564 <param name="reference_fasta" value="related_mitogenome_assembly.fasta"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
565 <param name="reference_genbank" value="related_mitogenome_assembly.gb"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
566 <param name="genetic_code" value="5"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
567 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
568 <output name="mitogenome_fasta" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
569 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
570 <has_size value="15684"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
571 <has_line line=">NC_016067.1_rc_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
572 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
573 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
574 <output name="mitogenome_genbank" ftype="genbank">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
575 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
576 <has_size value="31407"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
577 <has_line line="DEFINITION NC_016067.1_rc_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
578 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
579 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
580 </test>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
581 <!--Test 10-->
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
582 <test expect_num_outputs="6">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
583 <conditional name="operation_mode">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
584 <param name="command" value="mitohifi"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
585 <conditional name="input_option">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
586 <param name="input" value="pacbio"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
587 <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
588 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
589 <param name="reference_fasta" value="related_mitogenome.fasta"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
590 <param name="reference_genbank" value="related_mitogenome.gb"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
591 <param name="genetic_code" value="5"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
592 <param name="output_zip" value="True"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
593 </conditional>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
594 <output name="mitogenome_fasta" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
595 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
596 <has_size value="15337"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
597 <has_line line=">ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
598 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
599 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
600 <output name="mitogenome_genbank" ftype="genbank">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
601 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
602 <has_size value="30637"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
603 <has_line line="DEFINITION ptg000001c_rotated"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
604 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
605 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
606 <output name="hifiasm" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
607 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
608 <has_size value="4123737"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
609 <has_line line=">m64094_200908_163909/67999/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
610 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
611 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
612 <output name="hifiasm_filtered" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
613 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
614 <has_size value="4191948"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
615 <has_line line=">m64094_200908_163909/1605/ccs"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
616 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
617 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
bgruening
parents:
diff changeset
618 <output name="hifiasm_contigs" ftype="fasta">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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619 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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620 <has_size value="15329"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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621 <has_line line=">ptg000001c"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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622 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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623 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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624 <output name="zip_file" ftype="zip">
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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625 <assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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626 <has_size value="5418006" delta="100"/>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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627 </assert_contents>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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628 </output>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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629 </test>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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630 </tests>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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631 <help><![CDATA[
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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632 .. class:: infomark
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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633
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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634 **Purpose**
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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635
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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636
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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637 The dissemination of high-quality long reads (such as PacBio HiFi) makes the assembly of high-quality mitogenome straight forward. Because of the circular nature of the molecule, however, the mitocontig is usually assembled redundantly resulting in multiple-copy mitogenome-contigs. This pipeline was developed to finalise the assembly and annotation of the mitogenome. It will also dected different variants of the mitogenome present in your sample. At the end you are going to have all the variants assembled and annotated, and MitoHiFi.v2 is going to choose a final consensus sequence. In addtion, you will find an aligment of all the variants to facilitate your analysis of mitochondria heteroplasmy.
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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638
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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639 .. class:: infomark
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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640
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641 **Important parameter to change and test (-p)**
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642
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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643 Mitohifi is going to pull possible mito contigs by blasting your contigs with the close-related mito. The Default parameter -p is going to chose any contig which has 50% or more of its length in the blast match. This is the default because with invertebrate taxa from the Darwin Tree of Life we have been seeing that the repetitive portion of the mitogenomes is not very conserved between some taxa. In these cases, a more stringent -p ends up excluding real mito sequences. Nevertheless, if you are working with more conserved taxa - such as mammals and other vertebrates - use higher -p (such as 80 or 90) for better results.
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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644
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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645
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646 ]]> </help>
7c5e8ee8c0a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit fb6bc2755715fee453208273dd26b69da97ca65c"
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647 <expand macro="citations" />
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648 </tool>