Mercurial > repos > iuc > mitos2

annotate mitos2.xml @ 4:033755194fe9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
author iuc
date Wed, 01 Mar 2023 22:39:37 +0000
parents 624606f7c996
children e95d52d295d7
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4
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
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1 <tool id="mitos2" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>de-novo annotation of metazoan mitochondrial genomes</description>
3
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3 <xrefs>
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4 <xref type='bio.tools'>mitos</xref>
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5 </xrefs>
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6 <macros>
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7 <import>macros.xml</import>
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8 <token name="@MITOS_NAME@">MITOS2</token>
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033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
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9 <token name="@TOOL_VERSION@">2.1.3</token>
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
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10 <token name="@VERSION_SUFFIX@">0</token>
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11 </macros>
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
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14 </requirements>
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15 <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
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16 <command detect_errors="aggressive"><![CDATA[
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17 mkdir outdir &&
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18
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19 runmitos.py
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20 --input '$input'
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21 --code $code
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22 --outdir outdir
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23 --refdir '/'
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24 --refseqver '$refseqver.fields.path'
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25 $linear
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26 #for tpe in ["prot", "trna", "rrna", "intron", "oril", "orih"]
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27 #if not $tpe in str($advanced.featuretypes).split(',')
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28 --$tpe 0
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29 #end if
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30 #end for
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31 --finovl $advanced.finovl
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32 $advanced.best
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33 #set fragovl=float($advanced.fragovl)/100.0
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34 --fragovl $fragovl
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35 --fragfac $advanced.fragfac
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36
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37 --evalue $advanced_prot.evalue
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38 #set cutoff=float($advanced_prot.cutoff)/100.0
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39 --cutoff $cutoff
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40 --clipfac $advanced_prot.clipfac
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41 $advanced_prot.ncbicode
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42 $advanced_prot.alarab
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43 $advanced_prot.oldstst
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44 $advanced_ncrna.locandgloc
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45 --ncev $advanced_ncrna.ncev
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46 $advanced_ncrna.sensitive
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47 --maxtrnaovl $advanced_ncrna.maxtrnaovl
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48 --maxrrnaovl $advanced_ncrna.maxrrnaovl
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49
3
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50 #if not ("protein_plot" in $addoutputs or "ncRNA_plot" in $addoutputs):
0
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51 --noplots
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52 #end if
4
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
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53 #if "raw" in str($addoutputs).split(','):
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54 --zip
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55 #end if
0
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56
3
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57 #if "missing" in $addoutputs:
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58 > outdir/missing.txt
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59 #end if
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60 ]]></command>
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61 <inputs>
3
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62 <param argument="--input" label="Sequence" type="data" format="fasta" help="A single sequence in fasta formated sequence">
4
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63 <validator type="dataset_metadata_in_range" metadata_name="sequences" min="1" max="1"/>
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64 </param>
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65 <param argument="--code" label="Genetic code" type="select">
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66 <option value="2">Vertebrate (2)</option>
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67 <option value="4">Mold, Protozoan, Coelenteral (4)</option>
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68 <option value="5">Invertebrate (5)</option>
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69 <option value="9">Echinoderm, Flatworm (9)</option>
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70 <option value="13">Ascidian (13)</option>
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71 <option value="14">Alternative Flatworm (14)</option>
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72 </param>
3
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73 <param argument="--refseqver" label="Reference data" type="select" help="Contact the administrator of this Galaxy instance if you miss reference data">
0
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74 <options from_data_table="mitos">
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75 <filter type="static_value" value="mitos2" column="2"/>
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76 </options>
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77 <validator message="No reference annotation is available for MITOS2" type="no_options" />
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78 </param>
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79 <param argument="--linear" checked="false" label="Treat sequence as linear" type="boolean" truevalue="--linear" falsevalue=""/>
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80 <param name="addoutputs" type="select" multiple="true" label="Outputs">
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81 <option value="bed" selected="true">BED</option>
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82 <option value="mito" selected="false">mito</option>
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83 <option value="gff" selected="false">GFF file</option>
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84 <option value="seq" selected="false">SEQ</option>
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85 <option value="fas" selected="false">nucleotide FASTA</option>
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86 <option value="faa" selected="false">protein FASTA</option>
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87 <option value="geneorder" selected="false">geneorder</option>
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88 <option value="protein_plot" selected="false">Protein prediction plot</option>
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89 <option value="ncRNA_plot" selected="false">ncRNA prediction plot</option>
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90 <!--<option value="ncRNA_structure_ps_plots" selected="false">ncRNA structure plots - postscript</option>-->
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91 <option value="ncRNA_structure_svg_plots" selected="false">ncRNA structure plots - svg</option>
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92 <option value="raw" selected="false">zipped raw results</option>
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93 <option value="missing" selected="false">Missing genes</option>
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94 </param>
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95 <section name="advanced" title="Advanced options">
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96 <param name="featuretypes" label="Feature types" help="Feature types that should be predicted by MITOS (--noprot,--notrna,--norrna)" type="select" multiple="true">
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97 <option value="prot" selected="true">Protein coding genes</option>
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98 <option value="trna" selected="true">tRNAs</option>
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99 <option value="rrna" selected="true">rRNAs</option>
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100 <option value="intron" selected="false">Introns</option>
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101 <option value="oril" selected="false">Origin of light strand replication</option>
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102 <option value="orih" selected="false">Origin of heavy strand replication</option>
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103 </param>
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104 <param argument="--finovl" label="Final overlap (nt)" help="Maximum number of nucleotides by which genes of different types may overlap" type="integer" value="50" min="0"/>
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105 <param argument="--best" checked="false" label="Annotate only the best copy of each feature" type="boolean" truevalue="--best" falsevalue=""/>
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106 <param argument="--fragovl" label="Fragment overlap" help="Maximum allowed overlap of proteins in the query (in percent of the shorter query range) for two hits to be counted as fragments of the same gene" type="integer" value="20" min="0" max="100"/>
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107 <param argument="--fragfac" label="Fragment quality factor" help="Maximum factor by which fragments of the same protein may differ in their quality" type="float" min="0" value="10"/>
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108 </section>
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109 <section name="advanced_prot" title="Advanced options for protein coding gene prediction">
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110 <param argument="--evalue" label="BLAST E-value Exponent" help="Negation of the exponent of the E-value threshold used by BLAST, i.e. a value X gives an E-value of 10^(-X)" type="float" value="2" min="1"/>
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111 <param argument="--cutoff" label="Quality cutoff" help="Minimum allowed quality in % of the maximum quality value per reading frame" type="integer" value="50" min="0" max="100"/>
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112 <param argument="--clipfac" label="Clipping factor" help="Clip overlapping proteins with the same name that differ by less than the specified factor" type="float" value="10" min="0"/>
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113 <param argument="--ncbicode" checked="false" label="Use start/stop codons as in NCBI (default: learned start/stop codons)" type="boolean" truevalue="--ncbicode" falsevalue=""/>
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114 <param argument="--alarab" checked="false" label="Use the hmmer based method of Al Arab et al. 2016. This will consider the evalue, ncbicode, fragovl, fragfac" type="boolean" truevalue="--alarab" falsevalue=""/>
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115 <param argument="--oldstst" checked="false" label="Use the old start/stop prediction method of MITOS1" type="boolean" truevalue="--oldstst" falsevalue=""/>
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116 </section>
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117 <section name="advanced_ncrna" title="Advanced options for ncRNA gene prediction">
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118 <param argument="--locandgloc" checked="false" label="Run mitfi in glocal and local mode (default: local only)" type="boolean" truevalue="--locandgloc" falsevalue=""/>
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119 <param argument="--ncev" label="e-value to use for inferal fast mode" type="float" min="0" value="0.01"/>
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120 <param argument="--sensitive" checked="false" label="Use infernals sensitive mode only" type="boolean" truevalue="--sensitive" falsevalue=""/>
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121 <param argument="--maxtrnaovl" label="Allow tRNA overlap of up to X nt for mitfi" type="integer" value="50"/>
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122 <param argument="--maxrrnaovl" label="Allow rRNA overlap of up to X nt for mitfi" type="integer" value="50"/>
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123 </section>
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124 </inputs>
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125 <outputs>
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126 <data name="bedout" format="bed" from_work_dir="outdir/result.bed">
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127 <filter>"bed" in str(addoutputs)</filter>
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128 </data>
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129 <data name="mitoout" format="tabular" from_work_dir="outdir/result.mitos" label="${tool.name} on ${on_string}: mito">
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130 <filter>"mito" in str(addoutputs)</filter>
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131 </data>
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132 <data name="gffout" format="gff" from_work_dir="outdir/result.gff" label="${tool.name} on ${on_string}: GFF">
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133 <filter>"gff" in str(addoutputs)</filter>
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134 </data>
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135 <data name="seqout" format="txt" from_work_dir="outdir/result.seq" label="${tool.name} on ${on_string}: TBL">
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136 <filter>"seq" in str(addoutputs)</filter>
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137 </data>
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138 <data name="faa" format="fasta" from_work_dir="outdir/result.faa" label="${tool.name} on ${on_string}: aa FASTA">
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139 <filter>"faa" in str(addoutputs)</filter>
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140 </data>
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141 <data name="fas" format="fasta" from_work_dir="outdir/result.fas" label="${tool.name} on ${on_string}: nt FASTA">
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142 <filter>"fas" in str(addoutputs)</filter>
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143 </data>
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144 <data name="geneorderout" format="fasta" from_work_dir="outdir/result.geneorder" label="${tool.name} on ${on_string}: geneorder">
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145 <filter>"geneorder" in str(addoutputs)</filter>
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146 </data>
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147 <data name="protein_plot_out" format="pdf" from_work_dir="outdir/plots/prot.pdf" label="${tool.name} on ${on_string}: Protein prediction plot">
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148 <filter>"protein_plot" in str(addoutputs)</filter>
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149 </data>
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150 <data name="ncRNA_plot_out" format="pdf" from_work_dir="outdir/plots/rna.pdf" label="${tool.name} on ${on_string}: ncRNA prediction plot">
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151 <filter>"ncRNA_plot" in str(addoutputs)</filter>
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152 </data>
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153 <collection name="ncRNA_structure_plot_svg_out" type="list" label="${tool.name} on ${on_string}: ncRNA svg structure plots">
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154 <discover_datasets pattern="(?P&lt;name&gt;.+)\.svg" format="svg" directory="outdir/plots" />
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155 <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter>
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156 </collection>
4
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157 <data name="rawout" format="zip" from_work_dir="outdir.zip" label="${tool.name} on ${on_string}: raw data">
0
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158 <filter>"raw" in str(addoutputs)</filter>
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159 </data>
3
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160 <data name="missing_genes" format="txt" from_work_dir="outdir/missing.txt" label="${tool.name} on ${on_string}: missing genes">
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161 <filter>"missing" in str(addoutputs)</filter>
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162 </data>
0
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163 </outputs>
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164 <tests>
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165 <!-- default options -->
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166 <test expect_num_outputs="1">
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diff changeset
167 <param name="input" value="NC_012920.fasta"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
168 <param name="code" value="2"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
169 <param name="refseqver" value="mitos2-refdata" />
4
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
170 <output name="bedout" file="mitos2_NC_012920.bed" compare="re_match" ftype="bed"/>
0
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
171 <assert_command>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
172 <has_text text="--code 2"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
173 <has_text text="--finovl 50"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
174 <not_has_text text="--trna"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
175 <not_has_text text="--rrna"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
176 <not_has_text text="--prot"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
177 <has_text text="--intron 0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
178 <has_text text="--oril 0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
179 <has_text text="--orih 0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
180 <has_text text="--evalue 2.0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
181 <has_text text="--cutoff 0.5"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
182 <has_text text="--clipfac 10.0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
183 <not_has_text text="--best"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
184 <has_text text="--fragovl 0.2"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
185 <has_text text="--fragfac 10.0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
186 <has_text text="--ncev 0.01"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
187 <has_text text="--maxtrnaovl 50"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
188 <has_text text="--maxrrnaovl 50"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
189 <has_text text="--noplots"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
190 </assert_command>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
191 </test>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
192 <!-- different main options -->
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
193 <test expect_num_outputs="1">
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
194 <param name="input" value="NC_012920.fasta"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
195 <param name="code" value="5"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
196 <param name="refseqver" value="mitos2-refdata" />
4
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
197 <output name="bedout" ftype="bed">
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
198 <assert_contents>
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
199 <has_n_lines n="8"/>
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
200 </assert_contents>
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
201 </output>
0
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
202 <section name="advanced">
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
203 <param name="featuretypes" value="prot,trna,rrna,intron,oril,orih"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
204 <param name="finovl" value="49"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
205 <param name="best" value="true"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
206 <param name="fragovl" value="10"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
207 <param name="fragfac" value="9"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
208 </section>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
209 <assert_command>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
210 <has_text text="--code 5"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
211 <has_text text="--finovl 49"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
212 <not_has_text text="--trna"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
213 <not_has_text text="--rrna"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
214 <not_has_text text="--prot"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
215 <not_has_text text="--intron"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
216 <not_has_text text="--oril"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
217 <not_has_text text="--orih"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
218 <has_text text="--evalue 2.0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
219 <has_text text="--cutoff 0.5"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
220 <has_text text="--clipfac 10.0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
221 <has_text text="--best"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
222 <has_text text="--fragovl 0.1"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
223 <has_text text="--fragfac 9.0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
224 <has_text text="--ncev 0.01"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
225 <has_text text="--maxtrnaovl 50"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
226 <has_text text="--maxrrnaovl 50"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
227 <has_text text="--noplots"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
228 </assert_command>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
229 </test>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
230 <!-- different pcg and ncrn options -->
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
231 <test expect_num_outputs="11">
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
232 <param name="input" value="NC_012920.fasta"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
233 <param name="code" value="2"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
234 <param name="refseqver" value="mitos2-refdata" />
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
235 <section name="advanced_prot">
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
236 <param name="evalue" value="3"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
237 <param name="cutoff" value="49"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
238 <param name="clipfac" value="9"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
239 <param name="ncbicode" value="true"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
240 <param name="alarab" value="true"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
241 <param name="oldstst" value="true"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
242 </section>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
243 <section name="advanced_ncrna">
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
244 <!-- <param name="locandgloc" value="true"/> should be possible from 2.0.5 https://gitlab.com/Bernt/MITOS/-/commit/9b4c55c29961c307dce02ac0319dadbd76f6b9e5-->
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
245 <param name="ncev" value="0.1"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
246 <param name="sensitive" value="true"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
247 <param name="maxtrnaovl" value="51"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
248 <param name="maxrrnaovl" value="49"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
249 </section>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
250 <param name="addoutputs" value="bed,mito,gff,seq,fas,faa,geneorder,protein_plot,ncRNA_plot,ncRNA_structure_svg_plots,raw"/>
4
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
251 <output name="bedout" ftype="bed">
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
252 <assert_contents>
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
253 <has_n_lines n="18"/>
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
254 </assert_contents>
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
255 </output>
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
256 <output name="mitoout" file="mitos2_NC_012920.mitos" compare="re_match" ftype="tabular"/>
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
257 <output name="gffout" file="mitos2_NC_012920.gff" compare="re_match" ftype="gff"/>
0
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
258 <output name="seqout" file="mitos2_NC_012920.seq" ftype="txt"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
259 <output name="faa" file="mitos2_NC_012920.faa" ftype="fasta"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
260 <output name="fas" file="mitos2_NC_012920.fas" ftype="fasta"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
261 <output name="geneorderout" file="mitos2_NC_012920.geneorder" ftype="fasta"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
262 <output name="protein_plot_out" file="mitos2_NC_012920_prot.pdf" ftype="pdf" compare="sim_size"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
263 <output name="ncRNA_plot_out" file="mitos2_NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
264 <output name="rawout" ftype="zip">
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
265 <assert_contents>
4
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
266 <has_archive_member path="result.bed"/>
0
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
267 </assert_contents>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
268 </output>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
269 <output_collection name="ncRNA_structure_plot_svg_out" type="list" count="17"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
270 <assert_command>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
271 <has_text text="--code 2"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
272 <has_text text="--finovl 50"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
273 <not_has_text text="--trna"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
274 <not_has_text text="--rrna"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
275 <not_has_text text="--prot"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
276 <has_text text="--intron 0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
277 <has_text text="--oril 0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
278 <has_text text="--orih 0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
279 <has_text text="--evalue 3.0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
280 <has_text text="--cutoff 0.49"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
281 <has_text text="--clipfac 9.0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
282 <has_text text="--alarab"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
283 <has_text text="--oldstst"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
284 <has_text text="--ncbicode"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
285 <not_has_text text="--best"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
286 <has_text text="--fragovl 0.2"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
287 <has_text text="--fragfac 10.0"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
288 <!--<has_text text="\-\-locandgloc"/>-->
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
289 <has_text text="--ncev 0.1"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
290 <has_text text="--sensitive"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
291 <has_text text="--maxtrnaovl 51"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
292 <has_text text="--maxrrnaovl 49"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
293 <not_has_text text="--noplots"/>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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diff changeset
294 </assert_command>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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diff changeset
295 </test>
3
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
296 <!-- missing genes -->
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
297 <test expect_num_outputs="2">
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
298 <param name="input" value="NC_012920.fasta"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
299 <param name="code" value="2"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
300 <param name="refseqver" value="mitos2-refdata" />
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
301 <param name="addoutputs" value="bed,missing"/>
4
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
302 <output name="bedout" file="mitos2_NC_012920.bed" compare="re_match" ftype="bed"/>
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
303 <output name="missing_genes" ftype="txt">
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
304 <assert_contents>
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
305 <has_size value="167"/>
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
306 </assert_contents>
033755194fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
iuc
parents: 3
diff changeset
307 </output>
3
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
308 <assert_command>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
309 <has_text text="--code 2"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
310 <has_text text="--finovl 50"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
311 <not_has_text text="--trna"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
312 <not_has_text text="--rrna"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
313 <not_has_text text="--prot"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
314 <has_text text="--intron 0"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
315 <has_text text="--oril 0"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
316 <has_text text="--orih 0"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
317 <has_text text="--evalue 2.0"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
318 <has_text text="--cutoff 0.5"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
319 <has_text text="--clipfac 10.0"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
320 <not_has_text text="--best"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
321 <has_text text="--fragovl 0.2"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
322 <has_text text="--fragfac 10.0"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
323 <has_text text="--ncev 0.01"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
324 <has_text text="--maxtrnaovl 50"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
325 <has_text text="--maxrrnaovl 50"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
326 <has_text text="--noplots"/>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
iuc
parents: 2
diff changeset
327 </assert_command>
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
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parents: 2
diff changeset
328 </test>
0
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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diff changeset
329 </tests>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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diff changeset
330 <help>@COMMON_HELP@
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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diff changeset
331 <![CDATA[
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
332
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
333
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
334 **Advanced options**
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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diff changeset
335
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
336 - Feature types
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
337
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
338 Select the feature types that should be annotated. By default this is protein coding genes, tRNA and rRNA which is useful for metazoan mitogenomes. In addition also the replication origins of the light (OL) and heavy (OH) strand and introns can be annotated. The annotation of the replication origins is most useful for chordate mitogenomes. Introns are usually only found in mitogenomes of non-metazoans and basal Metazoa.
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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diff changeset
339
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
340 - Final overlap (nt)
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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diff changeset
341
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
342 Maximum number of nucleotides by which genes of different types may overlap. Applies to merging of the final predictions.
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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diff changeset
343
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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diff changeset
344 - Annotate only the best copy of each feature
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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345
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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346 If there are copies of the same feature type only the one with the lowest e-value (for ncRNAs and OL) or highest quality score (protein coding genes and OH)
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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347
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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348 - Fragment overlap
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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349
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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350 Maximum fraction (of the shorter feature) allowed that two hits overlap in the query to be counted as fragments.
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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351
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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352 - Fragment quality factor
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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353
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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354 Maximum factor by which fragments may differ in their quality scores. Higher values allow that parts of a gene can differ more in their quality.
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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355
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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356 **Advanced options for protein coding gene prediction**
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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357
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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358 - BLAST E-value Exponent
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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359
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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360 The statistical significance threshold for considering matches in the BLASTX search. The value entered here is the negation of the exponent of the E-value threshold that should be used by BLAST, i.e. a value X gives an E-value of 10^(-X).
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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361
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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362 - Quality cutoff
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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363
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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364 Minimum allowed quality value (in percent) of the maximum quality value per reading frame. A higher values correspond to shorter protein prediction and therefore reduced risk for conflicts with other features
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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365
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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366 - Clipping factor
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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367
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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368 Clipping is started if overlapping prediction of hits with the same name differ by less than a factor X in their quality value.
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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369
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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370 - use start/stop codons as in NCBI (default: learned start/stop codons)
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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371
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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372 Instead of the codon probabilities derived from the protein coding genes annotated in RefSeq the codons listed at NCBI taxonomy are used with equal probabilities (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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373
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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374 - Use the hmmer based method of Al Arab et al. 2016. This will consider the evalue, ncbicode, fragovl, fragfac parameters
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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375
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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376 Note: 1) this only works for Metazoa RefSeq release 63 reference data set. 2) This will only predict the protein coding genes that are typical for metazoan mitochondrial genomes.
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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377
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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378 - Use the old start/stop prediction method of MITOS1
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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379
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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380 The search for start and stop codons just takes the closest to the initial start / stop positions within 6aa (i.e. the method used in MITOS1)
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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381
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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382 **Advanced options for ncRNA gene prediction**
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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383
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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384 - Run mitfi in glocal and local mode (default: local only)
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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385
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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386 By default mitfi uses infernal's cmsearch in local search mode only. By enabling this option mitfi will invoke cmserach also in glocal mode if a feature is missing.
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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387
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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388 - e-value to use for inferal fast mode
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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389
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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390 The e-value passed to the first pass of cmsearch in the second pass (the sensitive search) an e-value of 0.1 is used.
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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391
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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392 - Use infernal's sensitive mode only
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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393
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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394 By default mitfi searches for ncRNAs using cmsearch's default fast mode first. If a ncRNA type is missing it is searched using the sensitive mode. This can be useful if low scoring copies are expected which might be missed when searching in the two stage mode.
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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395
3
624606f7c996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4
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396 - Allow tRNA/rRNA overlap of up to X nt for mitfi
0
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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397
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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398 Allow that a tRNA/rRNA overlaps with another feature by this number of nucleotides.
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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399
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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400 ]]></help>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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401 <citations>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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402 <citation type="doi">10.1093/nar/gkz833</citation>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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403 <citation type="doi">10.1016/j.ympev.2016.09.024</citation>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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404 </citations>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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405 </tool>
dd589aa77943 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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406