Mercurial > repos > iuc > funannotate_annotate

annotate funannotate_annotate.xml @ 0:a5baa4ff168d draft

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"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
author iuc
date Mon, 04 Oct 2021 19:39:38 +0000
parents
children aa19eaac7d4b
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1 <tool id="funannotate_annotate" name="Funannotate functional" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>annotation</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 <requirements>
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7 <expand macro="requirements" />
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8 </requirements>
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9 <version_command>funannotate check --show-versions</version_command>
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10 <command><![CDATA[
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11
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12 #if $uglyTestingHack == "true":
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13 ## funannotate_db contains some hard coded path, need to rewrite one for tests (not in real life when using data manager)
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14 ## Need to copy too as the test_data is read only on CI
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15 cp -r '${database.fields.path}' './hacked_database' &&
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16 sed -i.bak 's|/tmp/prout|'`pwd`'/hacked_database|' './hacked_database/trained_species/fly/info.json' &&
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17 #end if
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18
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19 funannotate annotate
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20
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21 #if $input.input_type == 'gbk'
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22 --genbank '${input.genbank}'
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23 #else
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24 --gff '${input.gff}'
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25 --fasta '${input.fasta}'
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26 --species '${input.species}'
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27 #end if
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28
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29 --out output
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30
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31 #if $uglyTestingHack == "true":
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32 --database `pwd`'/hacked_database'
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33 #else
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34 --database '$database.fields.path'
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35 #end if
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36
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37 #if $sbt:
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38 --sbt '${sbt}'
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39 #end if
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40
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41 #if $annotations:
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42 --annotations '${annotations}'
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43 #end if
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44
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45 #if $eggnog:
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46 --eggnog '${eggnog}'
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47 #end if
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48
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49 #if $antismash:
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50 --antismash '${antismash}'
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51 #end if
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52
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53 #if $iprscan:
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54 --iprscan '${iprscan}'
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55 #end if
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56
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57 #if $phobius:
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58 --phobius '${phobius}'
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59 #end if
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60
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61 --busco_db '${busco_db}'
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62
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63 --isolate '${isolate}'
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64 --strain '${strain}'
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65
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66 #if $rename:
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67 --rename '${rename}'
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68 #end if
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69 #if $fix:
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70 --fix '${fix}'
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71 #end if
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72 #if $remove:
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73 --remove '${remove}'
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74 #end if
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75
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76 --cpus \${GALAXY_SLOTS:-2}
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77
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78 &&
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79
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80 mv output/annotate_results/*.gbk out.gbk &&
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81 mv output/annotate_results/*.annotations.txt out.annotations.txt &&
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82 mv output/annotate_results/*.contigs.fsa out.contigs.fsa &&
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83 mv output/annotate_results/*.agp out.agp &&
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84 mv output/annotate_results/*.tbl out.tbl &&
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85 mv output/annotate_results/*.sqn out.sqn &&
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86 mv output/annotate_results/*.scaffolds.fa out.scaffolds.fa &&
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87 mv output/annotate_results/*.proteins.fa out.proteins.fa &&
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88 mv output/annotate_results/*.mrna-transcripts.fa out.mrna-transcripts.fa &&
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89 mv output/annotate_results/*.cds-transcripts.fa out.cds-transcripts.fa &&
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90 mv output/annotate_results/*.gff3 out.gff3 &&
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91 mv output/annotate_results/*.discrepency.report.txt out.discrepency.report.txt &&
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92 mv output/annotate_results/*.stats.json out.stats.json
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93 ]]></command>
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94 <inputs>
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95
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96 <conditional name="input">
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97 <param name="input_type" type="select" label="Input format">
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98 <option value="gbk" selected="True">GenBank (from 'Funannotate predict annotation' tool)</option>
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99 <option value="gff">GFF</option>
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100 </param>
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101 <when value="gbk">
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102 <param argument="--genbank" type="data" format="genbank" label="Genome annotation in genbank format" help="Output from 'Funannotate predict annotation' tool" />
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103 </when>
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104 <when value="gff">
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105 <param argument="--gff" type="data" format="gff3" label="Genome annotation in gff format" />
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106 <param argument="--fasta" type="data" format="fasta" label="Genome sequence" />
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107 <param argument="--species" type="text" optional="false" label="Name of the species to annotate" help="e.g. Genus species">
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108 <validator type="empty_field" />
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109 </param>
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110 </when>
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111 </conditional>
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112
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113
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114
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115 <param name="database" label="Funannotate database" type="select">
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116 <options from_data_table="funannotate">
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117 <column name="value" index="0" />
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118 <column name="name" index="1" />
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119 <column name="path" index="3" />
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120 <filter type="sort_by" column="0" />
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121 <filter type="static_value" column="2" value="1.0" />
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122 </options>
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123 </param>
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124
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125 <param argument="--sbt" type="data" format="sbt" optional="true" label="NCBI submission template file" help="Create it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ (or leave empty to use a default one, not suitable for submission at NCBI)" />
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126
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127 <param argument="--eggnog" type="data" format="tabular" optional="true" label="Eggnog-mapper annotations file" help="'annotations' output from 'eggNOG Mapper' tool" />
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128 <param argument="--antismash" type="data" format="genbank" optional="true" label="antiSMASH secondary metabolism results" help="Genbank output from 'Antismash' tool" />
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129 <param argument="--iprscan" type="data" format="xml" optional="true" label="InterProScan5 XML file" help="XML output from InterProScan" />
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130 <param argument="--phobius" type="data" format="tabular" optional="true" label="Phobius pre-computed results" />
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131
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132 <param argument="--busco_db" type="select" label="BUSCO models">
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133 <expand macro="busco_species"/>
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134 </param>
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135
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136 <param argument="--annotations" type="data" format="tabular" optional="true" label="Custom annotations" help="3 column tsv file" />
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137
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138 <param argument="--isolate" type="text" label="Isolate name" help="If relevant (e.g. Af293)" />
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139 <param argument="--strain" type="text" label="Strain name" help="If relevant (e.g. FGSCA4)" />
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140
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141 <param argument="--rename" type="text" label="locus_tag from NCBI to rename GFF gene models with" />
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142 <param argument="--fix" type="data" format="tabular" optional="true" label="Gene/Product names fixed" help="TSV: GeneID Name Product" />
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143 <param argument="--remove" type="data" format="tabular" optional="true" label="Gene/Product names to remove" help="TSV: Gene Product" />
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144
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145 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
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146 <option value="gbk" selected="true">Annotated genome (genbank)</option>
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147 <option value="annotations">TSV file of all annotations added to genome. (i.e. import into excel)</option>
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148 <option value="contigs_fsa">Multi-fasta file of contigs, split at gaps (use for NCBI submission)</option>
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149 <option value="agp">AGP file; showing linkage/location of contigs (use for NCBI submission)</option>
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150 <option value="tbl">NCBI tbl annotation file (use for NCBI submission)</option>
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151 <option value="sqn">NCBI Sequin genome file (use for NCBI submission)</option>
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152 <option value="scaffolds_fa">Multi-fasta file of scaffolds</option>
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153 <option value="proteins_fa">Multi-fasta file of protein coding genes</option>
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154 <option value="mrna_transcripts_fa">Multi-fasta file of transcripts (mRNA)</option>
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155 <option value="cds_transcripts_fa">Multi-fasta file of transcripts (CDS)</option>
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156 <option value="gff3">Annotation in GFF3 format</option>
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157 <option value="discrepency">tbl2asn summary report of annotated genome</option>
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158 <option value="stats">Statistics</option>
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159 <option value="must_fix">TSV file of Gene Name/Product deflines that failed to pass tbl2asn checks and must be fixed</option>
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160 <option value="need_curating">TSV file of Gene Name/Product defines that need to be curated</option>
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161 <option value="new_names_passed">TSV file of Gene Name/Product deflines that passed tbl2asn but are not in Gene2Products database.</option>
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162 </param>
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163
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164 <!-- Need this to change path in the test funannotate_db -->
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165 <param type="hidden" name="uglyTestingHack" value="" />
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166 </inputs>
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167 <outputs>
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168 <data name='gbk' format='genbank' label="${tool.name} on ${on_string}: annotated genome (genbank)" from_work_dir="out.gbk">
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169 <filter>outputs and 'gbk' in outputs</filter>
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170 </data>
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171 <data name='annot' format='tabular' label="${tool.name} on ${on_string}: all annotations" from_work_dir="out.annotations.txt">
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172 <filter>outputs and 'annotations' in outputs</filter>
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173 </data>
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174 <data name='contigs_fsa' format='fasta' label="${tool.name} on ${on_string}: contigs fasta, split at gaps" from_work_dir="out.contigs.fsa">
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175 <filter>outputs and 'contigs_fsa' in outputs</filter>
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176 </data>
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177 <data name='agp' format='tabular' label="${tool.name} on ${on_string}: NCBI tbl annotation file" from_work_dir="out.agp">
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178 <filter>outputs and 'agp' in outputs</filter>
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179 </data>
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180 <data name='tbl' format='txt' label="${tool.name} on ${on_string}: NCBI tbl annotation file" from_work_dir="out.tbl">
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181 <filter>outputs and 'tbl' in outputs</filter>
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182 </data>
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183 <data name='sqn' format='txt' label="${tool.name} on ${on_string}: NCBI Sequin genome" from_work_dir="out.sqn">
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184 <filter>outputs and 'sqn' in outputs</filter>
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185 </data>
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186 <data name='fa_scaffolds' format='fasta' label="${tool.name} on ${on_string}: scaffolds sequences" from_work_dir="out.scaffolds.fa">
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187 <filter>outputs and 'scaffolds_fa' in outputs</filter>
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188 </data>
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189 <data name='fa_proteins' format='fasta' label="${tool.name} on ${on_string}: protein sequences" from_work_dir="out.proteins.fa">
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190 <filter>outputs and 'proteins_fa' in outputs</filter>
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191 </data>
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192 <data name='fa_transcripts_mrna' format='fasta' label="${tool.name} on ${on_string}: transcript mRNA sequences" from_work_dir="out.mrna-transcripts.fa">
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193 <filter>outputs and 'mrna_transcripts_fa' in outputs</filter>
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194 </data>
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195 <data name='fa_transcripts_cds' format='fasta' label="${tool.name} on ${on_string}: transcript CDS sequences" from_work_dir="out.cds-transcripts.fa">
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196 <filter>outputs and 'cds_transcripts_fa' in outputs</filter>
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197 </data>
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198 <data name='gff3' format='gff3' label="${tool.name} on ${on_string}: annotation (GFF3)" from_work_dir="out.gff3">
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199 <filter>outputs and 'gff3' in outputs</filter>
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200 </data>
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201 <data name='tbl2asn_report' format='txt' label="${tool.name} on ${on_string}: tbl2asn summary report of annotated genome" from_work_dir="out.discrepency.report.txt">
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202 <filter>outputs and 'discrepency' in outputs</filter>
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203 </data>
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204 <data name='stats' format='json' label="${tool.name} on ${on_string}: stats" from_work_dir="out.stats.json">
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205 <filter>outputs and 'gbk' in outputs</filter>
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206 </data>
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207 <data name='must_fix' format='json' label="${tool.name} on ${on_string}: Gene Name/Product must-fix" from_work_dir="output/annotate_results/Gene2Products.must-fix.txt">
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208 <filter>outputs and 'must_fix' in outputs</filter>
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209 </data>
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210 <data name='need_curating' format='json' label="${tool.name} on ${on_string}: Gene Name/Product need-curating" from_work_dir="output/annotate_results/Gene2Products.need-curating.txt">
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211 <filter>outputs and 'need_curating' in outputs</filter>
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212 </data>
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213 <data name='new_names_passed' format='json' label="${tool.name} on ${on_string}: Gene Name/Product new-names-passed" from_work_dir="output/annotate_results/Gene2Products.new-names-passed.txt">
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214 <filter>outputs and 'new_names_passed' in outputs</filter>
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215 </data>
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216 </outputs>
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217 <tests>
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diff changeset
218 <test>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
219 <conditional name="input">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
220 <param name="input_type" value="gbk" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
221 <param name="genbank" value="predict_augustus/Genus_species.gbk" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
222 </conditional>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
223 <param name="database" value="2021-07-20-120000" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
224 <param name="busco_db" value="insecta" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
225 <param name="outputs" value="gbk,annotations,contigs_fsa,agp,tbl,sqn,scaffolds_fa,proteins_fa,mrna_transcripts_fa,cds_transcripts_fa,gff3,discrepency,stats,must_fix,need_curating,new_names_passed" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
226 <output name="gbk">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
227 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
228 <has_text text="DEFINITION Genus species." />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
229 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
230 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
231 <output name="annot">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
232 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
233 <has_text text="EC_number" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
234 <has_text text="EOG090W0T3K" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
235 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
236 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
237 <output name="contigs_fsa">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
238 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
239 <has_text text=">contig_1" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
240 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
241 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
242 <output name="agp">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
243 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
244 <has_text text="contig_1" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
245 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
246 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
247 <output name="tbl">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
248 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
249 <has_text text="locus_tag" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
250 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
251 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
252 <output name="sqn">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
253 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
254 <has_text text="Seq-submit" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
255 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
256 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
257 <output name="fa_scaffolds">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
258 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
259 <has_text text=">sample" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
260 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
261 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
262 <output name="fa_proteins">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
263 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
264 <has_text text=">FUN_000001-T1 FUN_000001" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
265 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
266 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
267 <output name="fa_transcripts_mrna">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
268 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
269 <has_text text=">FUN_000001-T1 FUN_000001" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
270 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
271 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
272 <output name="fa_transcripts_cds">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
273 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
274 <has_text text=">FUN_000001-T1 FUN_000001" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
275 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
276 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
277 <output name="gff3">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
278 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
279 <has_text text="ID=FUN_000001;" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
280 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
281 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
282 <output name="tbl2asn_report">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
283 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
284 <has_text text="Discrepancy Report Results" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
285 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
286 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
287 <output name="stats">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
288 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
289 <has_text text="avg_gene_length" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
290 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
291 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
292 <output name="must_fix">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
293 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
294 <has_text text="tbl2asn Error" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
295 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
296 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
297 <output name="need_curating">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
298 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
299 <has_text text="Original Description" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
300 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
301 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
302 <output name="new_names_passed">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
303 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
304 <has_text text="Passed Description" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
305 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
306 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
307 </test>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
308 <test>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
309 <conditional name="input">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
310 <param name="input_type" value="gff" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
311 <param name="gff" value="predict_augustus/Genus_species.gff3" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
312 <param name="fasta" value="genome.fa" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
313 <param name="species" value="Genus species" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
314 </conditional>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
315 <param name="database" value="2021-07-20-120000" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
316 <param name="busco_db" value="insecta" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
317 <param name="outputs" value="gbk,annotations,contigs_fsa,agp,tbl,sqn,scaffolds_fa,proteins_fa,mrna_transcripts_fa,cds_transcripts_fa,gff3,discrepency,stats,must_fix,need_curating,new_names_passed" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
318 <output name="gbk">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
319 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
320 <has_text text="DEFINITION Genus species." />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
321 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
322 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
323 <output name="annot">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
324 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
325 <has_text text="EC_number" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
326 <has_text text="EOG090W0T3K" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
327 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
328 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
329 <output name="contigs_fsa">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
330 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
331 <has_text text=">contig_1" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
332 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
333 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
334 <output name="agp">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
335 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
336 <has_text text="contig_1" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
337 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
338 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
339 <output name="tbl">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
340 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
341 <has_text text="locus_tag" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
342 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
343 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
344 <output name="sqn">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
345 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
346 <has_text text="Seq-submit" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
347 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
348 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
349 <output name="fa_scaffolds">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
350 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
351 <has_text text=">sample" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
352 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
353 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
354 <output name="fa_proteins">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
355 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
356 <has_text text=">FUN_000001-T1 FUN_000001" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
357 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
358 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
359 <output name="fa_transcripts_mrna">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
360 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
361 <has_text text=">FUN_000001-T1 FUN_000001" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
362 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
363 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
364 <output name="fa_transcripts_cds">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
365 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
366 <has_text text=">FUN_000001-T1 FUN_000001" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
367 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
368 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
369 <output name="gff3">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
370 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
371 <has_text text="ID=FUN_000001;" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
372 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
373 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
374 <output name="tbl2asn_report">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
375 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
376 <has_text text="Discrepancy Report Results" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
377 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
378 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
379 <output name="stats">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
380 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
381 <has_text text="avg_gene_length" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
382 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
383 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
384 <output name="must_fix">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
385 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
386 <has_text text="tbl2asn Error" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
387 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
388 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
389 <output name="need_curating">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
390 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
391 <has_text text="Original Description" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
392 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
393 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
394 <output name="new_names_passed">
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
395 <assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
396 <has_text text="Passed Description" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
397 </assert_contents>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
398 </output>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
399 </test>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
400 </tests>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
401 <help><![CDATA[
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
402 Funannotate_ annotate
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
403 ---------------------
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
404
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
405 Funannotate_ is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
406
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
407 This script functionally annotates the results from funannotate predict. It pulls
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
408 annotation from PFAM, InterPro, EggNog, UniProtKB, MEROPS, CAZyme, and GO ontology.
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
409
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
410 .. _Funannotate: http://funannotate.readthedocs.io
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
411 ]]></help>
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
412 <expand macro="citations" />
a5baa4ff168d "planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
iuc
parents:
diff changeset
413 </tool>