Mercurial > repos > iuc > mitos

annotate mitos.xml @ 2:1f4933f5a323 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
author iuc
date Wed, 02 Jun 2021 18:39:05 +0000
parents 39b6485e2d34
children f20804c311de
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2
1f4933f5a323 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
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1 <tool id="mitos" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
0
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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2 <description>de-novo annotation of metazoan mitochondrial genomes</description>
2
1f4933f5a323 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
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3 <macros>
1f4933f5a323 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
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4 <import>macros.xml</import>
1f4933f5a323 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
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5 <token name="@MITOS_NAME@">MITOS</token>
1f4933f5a323 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
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6 <token name="@TOOL_VERSION@">1.0.5</token>
1f4933f5a323 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
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7 <token name="@VERSION_SUFFIX@">1</token>
1f4933f5a323 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
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8 </macros>
1f4933f5a323 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
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9 <requirements>
1f4933f5a323 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
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10 <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
1f4933f5a323 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
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11 <requirement type="package">zip</requirement>
0
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12 </requirements>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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13 <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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14 <command detect_errors="aggressive"><![CDATA[
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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15 mkdir outdir &&
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16
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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17 runmitos.py
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18 --input '$input'
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19 --code $code
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20 --outdir outdir
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21 --refdir '$refdir.fields.path'
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22 #for tpe in ["prot", "trna", "rrna"]
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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23 #if not $tpe in str($advanced.featuretypes).split(',')
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24 --no$tpe
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25 #end if
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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26 #end for
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27 --finovl $advanced.finovl
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28 --evalue $advanced_prot.evalue
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29 --cutoff $advanced_prot.cutoff
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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30 #set maxovl=float($advanced_prot.maxovl)/100.0
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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31 --maxovl $maxovl
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32 --clipfac $advanced_prot.clipfac
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33 #set fragovl=float($advanced_prot.fragovl)/100.0
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34 --fragovl $fragovl
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35 --fragfac $advanced_prot.fragfac
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36 --ststrange $advanced_prot.ststrange
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37
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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38 #if "raw" in str($addoutputs).split(','):
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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39 && zip -9 -y -r output.zip outdir/ > /dev/null
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40 #end if
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41 ]]></command>
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42 <inputs>
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43 <param argument="--input" label="sequence" type="data" format="fasta" help="a single sequence in fasta formated sequence">
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44 <options options_filter_attribute="metadata.sequences">
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45 <filter type="add_value" value="1"/>
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46 </options>
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47 </param>
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48 <param argument="--code" label="Genetic code" type="select">
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49 <option value="2">Vertebrate (2)</option>
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50 <option value="4">Mold, Protozoan, Coelenteral (4)</option>
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51 <option value="5">Invertebrate (5)</option>
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52 <option value="9">Echinoderm, Flatworm (9)</option>
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53 <option value="13">Ascidian (13)</option>
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54 <option value="14">Alternative Flatworm (14)</option>
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55 </param>
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56 <param argument="--refdir" label="Reference data" type="select" help="contact the administrator of this Galaxy instance if you miss reference data">
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57 <options from_data_table="mitos">
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58 <filter type="static_value" value="mitos" column="2"/>
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59 </options>
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60 <validator message="No reference annotation is available for MITOS" type="no_options" />
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61 </param>
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62 <param name="addoutputs" type="select" multiple="true" label="Outputs">
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63 <option value="bed" selected="true">BED</option>
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64 <option value="mito" selected="false">mito</option>
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65 <option value="gff" selected="false">GFF file</option>
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66 <option value="seq" selected="false">SEQ</option>
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67 <option value="fas" selected="false">nucleotide FASTA</option>
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68 <option value="faa" selected="false">protein FASTA</option>
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69 <option value="geneorder" selected="false">geneorder</option>
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70 <option value="protein_plot" selected="false">Protein prediction plot</option>
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71 <option value="ncRNA_plot" selected="false">ncRNA prediction plot</option>
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72 <!--<option value="ncRNA_structure_ps_plots" selected="false">ncRNA structure plots - postscript</option>-->
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73 <option value="ncRNA_structure_svg_plots" selected="false">ncRNA structure plots - svg</option>
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74 <option value="raw" selected="false">zipped raw results</option>
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75 </param>
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76 <section name="advanced" title="Advanced options">
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77 <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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78 <option value="prot" selected="true">Protein coding genes</option>
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79 <option value="trna" selected="true">tRNAs</option>
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80 <option value="rrna" selected="true">rRNAs</option>
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81 </param>
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82 <param argument="--finovl" label="Final overlap (nt)" help="Maximum number of nucleotides by which genes of different types may overlap" type="integer" value="35" min="0"/>
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83 </section>
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84 <section name="advanced_prot" title="Advanced options for protein coding gene prediction">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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85 <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="0"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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86 <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"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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87 <param argument="--maxovl" label="Maximum overlap" help="Maximum allowed overlap of proteins in percent of the smaller feature " type="integer" value="20" min="0" max="100"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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88 <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"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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89 <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"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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90 <param argument="--fragfac" label="Fragment quality factor" help="Maximum factor by which fragments of the same protein may differ in their quality" type="float" value="10"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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91 <param argument="--ststrange" label="Start/stop range" help="Number of aminoacids searched for start and stop codon of proteins" type="integer" value="6"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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92 </section>
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93 </inputs>
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94 <outputs>
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95 <data name="bedout" format="bed" from_work_dir="outdir/result.bed">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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96 <filter>"bed" in str(addoutputs)</filter>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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97 </data>
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98 <data name="mitoout" format="tabular" from_work_dir="outdir/result" label="${tool.name} on ${on_string}: mito">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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99 <filter>"mito" in str(addoutputs)</filter>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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100 </data>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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101 <data name="gffout" format="gff" from_work_dir="outdir/result.gff" label="${tool.name} on ${on_string}: GFF">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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102 <filter>"gff" in str(addoutputs)</filter>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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103 </data>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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104 <data name="seqout" format="txt" from_work_dir="outdir/result.seq" label="${tool.name} on ${on_string}: TBL">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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105 <filter>"seq" in str(addoutputs)</filter>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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106 </data>
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107 <data name="fasout" format="fasta" from_work_dir="outdir/result.fas" label="${tool.name} on ${on_string}: nt FASTA">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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108 <filter>"fas" in str(addoutputs)</filter>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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109 </data>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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110 <data name="faaout" format="fasta" from_work_dir="outdir/result.faa" label="${tool.name} on ${on_string}: aa FASTA">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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111 <filter>"faa" in str(addoutputs)</filter>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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112 </data>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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113 <data name="geneorderout" format="fasta" from_work_dir="outdir/result.geneorder" label="${tool.name} on ${on_string}: geneorder">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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114 <filter>"geneorder" in str(addoutputs)</filter>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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115 </data>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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116 <data name="protein_plot_out" format="pdf" from_work_dir="outdir/plots/prot.pdf" label="${tool.name} on ${on_string}: Protein prediction plot">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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117 <filter>"protein_plot" in str(addoutputs)</filter>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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118 </data>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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119 <data name="ncRNA_plot_out" format="pdf" from_work_dir="outdir/plots/rna.pdf" label="${tool.name} on ${on_string}: ncRNA prediction plot">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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120 <filter>"protein_plot" in str(addoutputs)</filter>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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121 </data>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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122 <!--<collection name="ncRNA_structure_plot_ps_out" type="list" label="${tool.name} on ${on_string}: ncRNA postscript structure plots">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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123 <discover_datasets pattern="(?P&lt;name&gt;.+)\.ps" format="ps" directory="outdir/plots" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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124 <filter>"ncRNA_structure_ps_plots" in str(addoutputs)</filter>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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125 </collection>-->
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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126 <collection name="ncRNA_structure_plot_svg_out" type="list" label="${tool.name} on ${on_string}: ncRNA svg structure plots">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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127 <discover_datasets pattern="(?P&lt;name&gt;.+)\.svg" format="svg" directory="outdir/plots" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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128 <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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129 </collection>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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130 <data name="rawout" format="zip" from_work_dir="output.zip" label="${tool.name} on ${on_string}: raw data">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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131 <filter>"raw" in str(addoutputs)</filter>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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132 </data>
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133 </outputs>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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134 <tests>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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135 <!-- default options -->
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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136 <test expect_num_outputs="1">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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137 <param name="input" value="NC_012920.fasta"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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138 <param name="code" value="2"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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139 <param name="refdir" value="mitos1-refdata" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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140 <output name="bedout" file="NC_012920.bed" ftype="bed"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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141 <assert_command>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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142 <has_text text="--code 2"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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143 <has_text text="--finovl 35"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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144 <has_text text="--evalue 2.0"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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145 <has_text text="--cutoff 50"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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146 <has_text text="--maxovl 0.2"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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147 <has_text text="--clipfac 10.0"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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148 <has_text text="--fragovl 0.2"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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149 <has_text text="--fragfac 10.0"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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150 <has_text text="--ststrange 6"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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151 </assert_command>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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152 </test>
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153 <!-- default options, add outputs -->
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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154 <test expect_num_outputs="11">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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155 <param name="input" value="NC_012920.fasta"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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156 <param name="code" value="2"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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157 <param name="refdir" value="mitos1-refdata" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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158 <param name="addoutputs" value="bed,mito,gff,seq,fas,faa,raw,geneorder,protein_plot,ncRNA_plot,ncRNA_structure_svg_plots"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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159 <output name="bedout" file="NC_012920.bed" ftype="bed"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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160 <output name="mitoout" file="NC_012920.mito" ftype="tabular" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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161 <output name="gffout" file="NC_012920.gff" ftype="gff" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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162 <output name="seqout" file="NC_012920.seq" ftype="txt" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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163 <output name="fasout" file="NC_012920.fas" ftype="fasta" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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diff changeset
164 <output name="faaout" file="NC_012920.faa" ftype="fasta" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
165 <output name="rawout" ftype="zip">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
166 <assert_contents>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
167 <has_archive_member path=".*/result.bed"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
168 </assert_contents>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
169 </output>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
170 <output name="geneorderout" file="NC_012920.geneorder" ftype="fasta" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
171 <output name="protein_plot_out" file="NC_012920_prot.pdf" ftype="pdf" compare="sim_size"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
172 <output name="ncRNA_plot_out" file="NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
173 <output_collection name="ncRNA_structure_plot_svg_out" type="list" count="24">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
174 <element name="trnA-5586-5654" file="NC_012920_trnA.svg" ftype="svg" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
175 </output_collection>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
176 <assert_command>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
177 <has_text text="--code 2"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
178 <has_text text="--finovl 35"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
179 <has_text text="--evalue 2.0"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
180 <has_text text="--cutoff 50"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
181 <has_text text="--maxovl 0.2"/>
39b6485e2d34 "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"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
183 <has_text text="--fragovl 0.2"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
184 <has_text text="--fragfac 10.0"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
185 <has_text text="--ststrange 6"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
186 </assert_command>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
187 </test>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
188 <!-- no rRNA, and advanced options -->
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
189 <test expect_num_outputs="1">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
190 <param name="input" value="NC_012920.fasta"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
191 <param name="code" value="2"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
192 <param name="refdir" value="mitos1-refdata" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
193 <param name="advanced|featuretypes" value="prot,trna" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
194 <param name="advanced|finovl" value="50" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
195 <output name="bedout" file="NC_012920.bed" ftype="bed" compare="sim_size"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
196 <assert_command>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
197 <has_text text="--code 2"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
198 <has_text text="--norrna"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
199 <has_text text="--finovl 50"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
200 </assert_command>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
201 </test>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
202 <!-- no rRNA, no tRNA; advanced protein options -->
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
203 <test expect_num_outputs="1">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
204 <param name="input" value="NC_012920.fasta"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
205 <param name="code" value="5"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
206 <param name="refdir" value="mitos1-refdata" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
207 <param name="advanced|featuretypes" value="prot" />
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
208 <param name="advanced_prot|evalue" value="3"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
209 <param name="advanced_prot|cutoff" value="40"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
210 <param name="advanced_prot|maxovl" value="30"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
211 <param name="advanced_prot|clipfac" value="5"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
212 <param name="advanced_prot|fragovl" value="15"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
213 <param name="advanced_prot|fragfac" value="11"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
214 <param name="advanced_prot|ststrange" value="12"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
215 <param name="addoutputs" value="bed"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
216 <output name="bedout" file="NC_012920.bed" ftype="bed" compare="sim_size"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
217 <assert_command>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
218 <has_text text="--code 5"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
219 <has_text text="--evalue 3"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
220 <has_text text="--cutoff 40"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
221 <has_text text="--maxovl 0.3"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
222 <has_text text="--clipfac 5.0"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
223 <has_text text="--fragovl 0.15"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
224 <has_text text="--fragfac 11.0"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
225 <has_text text="--ststrange 12"/>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
226 </assert_command>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
227 </test>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
228 </tests>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
229 <help>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
230 @COMMON_HELP@
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
231 <![CDATA[
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
232 ]]></help>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
233 <citations>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
234 <citation type="doi">10.1016/j.ympev.2012.08.023</citation>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
235 </citations>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
236 </tool>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
diff changeset
237