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annotate busco.xml @ 5:1440ae06552f draft

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planemo upload commit 85b6db2b28551a663821655c13134b47290140d2
author iuc
date Mon, 13 May 2019 09:17:19 -0400
parents 5ecdeca79a0d
children 1e62c28ba91d
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1 <tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy1">
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2 <description>assess genome assembly and annotation completeness</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">3.0.2</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
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8 <requirement type="package" version="3.5.1">r-base</requirement>
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9 <requirement type="package" version="3.3.2">augustus</requirement>
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10 </requirements>
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11 <command><![CDATA[
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12 export BUSCO_CONFIG_FILE='busco_config.ini' &&
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13 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
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14 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
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15 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
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16
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17 #if $adv.aug_prediction.augustus_mode == 'history':
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18 ## Using an augustus model from history, we need to unzip it and let augustus find it
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19 mkdir -p 'augustus_dir/species/' &&
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20 tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null &&
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21 #end if
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22
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23 run_BUSCO.py
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24 --in '${input}'
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25 --lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}'
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26 --mode '${mode}'
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27 -o busco_galaxy
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28 --cpu \${GALAXY_SLOTS:-4}
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29 --evalue ${adv.evalue}
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30 ${adv.long}
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31 --limit ${adv.limit}
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32 #if $adv.aug_prediction.augustus_mode == 'builtin':
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33 --species '${adv.aug_prediction.augustus_species}'
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34 #else if $adv.aug_prediction.augustus_mode == 'history':
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35 --species local
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36 #end if
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37 --tarzip
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38 ]]></command>
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39
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40 <inputs>
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41 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />
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42 <param argument="--mode" type="select" label="Mode">
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43 <option value="geno">Genome</option>
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44 <option value="tran">Transcriptome</option>
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45 <option value="prot">Proteome</option>
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46 </param>
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47
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48 <param argument="--lineage_path" type="select" label="Lineage">
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49 <options from_data_table="busco">
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50 <filter type="sort_by" column="2" />
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51 <validator type="no_options" message="No indexes are available" />
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52 </options>
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53 </param>
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54
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55 <section name="adv" title="Advanced Options" expanded="False">
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56 <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/>
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57 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
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58
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59 <conditional name="aug_prediction">
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60 <param name="augustus_mode" type="select" label="Augustus species model">
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61 <option value="no" selected="true">Use the default species for selected lineage</option>
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62 <option value="builtin">Use another predefined species model</option>
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63 <option value="history">Use a custom species model</option>
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64 </param>
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65 <when value="no"/>
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66 <when value="history">
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67 <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>
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68 </when>
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69 <when value="builtin">
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70 <param name="augustus_species" type="select" label="Augustus species model">
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71 <!-- If you update this list, please also update it in maker and augustus tools (../maker/maker.xml and ../augustus/augustus.xml) -->
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72 <option value="human">Homo sapiens</option>
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73 <option value="fly">Drosophila melanogaster</option>
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74 <option value="arabidopsis">Arabidopsis thaliana</option>
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75 <option value="brugia ">Brugia malayi</option>
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76 <option value="aedes">Aedes aegypti</option>
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77 <option value="tribolium2012">Tribolium castaneum</option>
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78 <option value="schistosoma">Schistosoma mansoni</option>
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79 <option value="tetrahymena">Tetrahymena thermophila</option>
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80 <option value="galdieria">Galdieria sulphuraria</option>
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81 <option value="maize">Zea mays</option>
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82 <option value="toxoplasma">Toxoplasma gondii</option>
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83 <option value="caenorhabditis ">Caenorhabditis elegans</option>
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84 <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
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85 <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
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86 <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
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87 <option value="aspergillus_terreus">Aspergillus terreus</option>
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88 <option value="botrytis_cinerea ">Botrytis cinerea</option>
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89 <option value="candida_albicans ">Candida albicans</option>
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90 <option value="candida_guilliermondii ">Candida guilliermondii</option>
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91 <option value="candida_tropicalis ">Candida tropicalis</option>
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92 <option value="chaetomium_globosum">Chaetomium globosum</option>
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93 <option value="coccidioides_immitis">Coccidioides immitis</option>
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94 <option value="coprinus">Coprinus cinereus</option>
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95 <option value="coprinus_cinereus">Coprinus cinereus</option>
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96 <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
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97 <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
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98 <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
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99 <option value="cryptococcus">Cryptococcus neoformans</option>
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100 <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
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101 <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
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102 <option value="eremothecium_gossypii">Eremothecium gossypii</option>
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103 <option value="fusarium_graminearum ">Fusarium graminearum</option>
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104 <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
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105 <option value="histoplasma">Histoplasma capsulatum</option>
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106 <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
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107 <option value="laccaria_bicolor ">Laccaria bicolor</option>
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108 <option value="lamprey">Petromyzon marinus</option>
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109 <option value="leishmania_tarentolae">Leishmania tarentolae</option>
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110 <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
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111 <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
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112 <option value="neurospora_crassa">Neurospora crassa</option>
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113 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
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114 <option value="pichia_stipitis">Pichia stipitis</option>
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115 <option value="rhizopus_oryzae">Rhizopus oryzae</option>
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116 <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
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117 <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
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118 <option value="saccharomyces">Saccharomyces cerevisiae</option>
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119 <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
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120 <option value="trichinella">Trichinella spiralis</option>
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121 <option value="ustilago_maydis">Ustilago maydis</option>
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122 <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
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123 <option value="nasonia">Nasonia vitripennis</option>
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124 <option value="tomato">Solanum lycopersicum</option>
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125 <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
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126 <option value="amphimedon">Amphimedon queenslandica</option>
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127 <option value="pneumocystis">Pneumocystis jirovecii</option>
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128 <option value="chicken">Gallus gallus domesticus (chicken)</option>
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129 <option value="cacao">Theobroma cacao (cacao)</option>
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130 <option value="heliconius_melpomene1">Heliconius melpomene</option>
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131 <option value="xenoturbella">Xenoturbella</option>
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132 <option value="E_coli_K12">E coli K12</option>
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133 <option value="c_elegans_trsk">c elegans trsk</option>
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134 <option value="camponotus_floridanus">Camponotus floridanus</option>
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135 <option value="coyote_tobacco">Coyote tobacco</option>
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136 <option value="s_aureus">Staphylococcus aureus</option>
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137 <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
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138 <option value="wheat">wheat</option>
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139 <option value="zebrafish">Danio rerio</option>
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140 <option value="anidulans">Aspergillus nidulans</option>
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141 <option value="bombus_impatiens1">Bombus impatiens1</option>
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142 <option value="bombus_terrestris2">Bombus terrestris2</option>
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143 <option value="botrytis_cinerea">Botrytis cinerea</option>
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144 <option value="brugia_malayi">Brugia malayi</option>
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145 <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
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146 <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
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147 <option value="culex_pipiens">Culex pipiens</option>
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148 <option value="elephant_shark">Callorhinchus milii</option>
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149 <option value="honeybee1">Apis mellifera</option>
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150 <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
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151 <option value="pea_aphid">Acyrthosiphon pisum</option>
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152 <option value="rhodnius_prolixus">Rhodnius prolixus</option>
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153 <option value="ustilago_maydis">Ustilago maydis</option>
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154 <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
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155 <option value="verticillium_longisporum1">Verticillium longisporum1</option>
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156 <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
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157 <option value="adorsata">adorsata</option>
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158 <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
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159 <option value="maker2_athal1">maker2_athal1</option>
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160 <option value="maker2_c_elegans1">maker2_c_elegans1</option>
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161 <option value="maker2_dmel1">maker2_dmel1</option>
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162 <option value="maker2_spomb1">maker2_spomb1</option>
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163 <option value="parasteatoda">parasteatoda</option>
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164 <option value="rice">rice</option>
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165 <option value="schistosoma2">schistosoma2</option>
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166 <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
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167 </param>
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168 </when>
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169 </conditional>
0
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170 <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/>
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171 </section>
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172 </inputs>
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173 <outputs>
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174 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy.txt"/>
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175 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="run_busco_galaxy/full_table_busco_galaxy.tsv"/>
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176 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_busco_list_busco_galaxy.tsv"/>
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177 </outputs>
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178 <tests>
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179 <test>
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180 <param name="input" value="genome.fa"/>
2
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181 <param name="lineage_path" value="arthropoda"/>
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182 <param name="mode" value="geno"/>
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183 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
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184 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
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185 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
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186 </test>
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187 <test>
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188 <param name="input" value="proteome.fa"/>
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189 <param name="lineage_path" value="arthropoda"/>
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190 <param name="mode" value="prot"/>
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191 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4"/>
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192 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4"/>
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193 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
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194 </test>
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195 <test>
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196 <param name="input" value="transcriptome.fa"/>
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197 <param name="lineage_path" value="arthropoda"/>
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198 <param name="mode" value="tran"/>
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199 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/>
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200 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/>
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201 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
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202 </test>
2
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203 <test>
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204 <param name="input" value="genome.fa"/>
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205 <param name="lineage_path" value="arthropoda"/>
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206 <param name="mode" value="geno"/>
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207 <param name="adv|aug_prediction|augustus_mode" value="builtin"/>
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208 <param name="adv|aug_prediction|augustus_species" value="human"/>
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209 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
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210 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
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211 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
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212 </test>
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213 <test>
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214 <param name="input" value="genome.fa"/>
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215 <param name="lineage_path" value="arthropoda"/>
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216 <param name="mode" value="geno"/>
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217 <param name="adv|aug_prediction|augustus_mode" value="history"/>
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218 <param name="adv|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>
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219 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
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220 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
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221 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
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222 </test>
0
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223 </tests>
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224 <help>
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225 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
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226
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227 .. _BUSCO: http://busco.ezlab.org/
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228 </help>
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229 <citations>
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230 <citation type="doi">doi:10.1093/bioinformatics/btv351</citation>
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231 </citations>
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232 </tool>