mitos2: mitos2.xml annotate

annotate mitos2.xml @ 3:994e1ce9f4d5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

author	iuc
date	Wed, 01 Sep 2021 07:40:48 +0000
parents	07f0df25bd0c
children	07caa60ff5c4

rev	line source
2 07f0df25bd0c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68" iuc parents: 0 diff changeset	1 <tool id="mitos2" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0 64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	2 <description>de-novo annotation of metazoan mitochondrial genomes</description>
3 994e1ce9f4d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 2 diff changeset	3 <xrefs>
994e1ce9f4d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 2 diff changeset	4 <xref type='bio.tools'>mitos</xref>
994e1ce9f4d5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 2 diff changeset	5 </xrefs>
0 64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	6 <macros>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	7 <import>macros.xml</import>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	8 <token name="@MITOS_NAME@">MITOS2</token>
2 07f0df25bd0c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68" iuc parents: 0 diff changeset	9 <token name="@TOOL_VERSION@">2.0.6</token>
07f0df25bd0c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68" iuc parents: 0 diff changeset	10 <token name="@VERSION_SUFFIX@">1</token>
0 64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	11 </macros>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	12 <requirements>
2 07f0df25bd0c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68" iuc parents: 0 diff changeset	13 <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
0 64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	14 <requirement type="package">zip</requirement>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	15 </requirements>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	16 <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	17 <command detect_errors="aggressive"><![CDATA[
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	18 mkdir outdir &&
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	19
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	20 runmitos.py
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	21 --input '$input'
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	22 --code $code
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	23 --outdir outdir
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	24 --refdir '/'
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	25 --refseqver '$refseqver.fields.path'
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	26 $linear
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	27 #for tpe in ["prot", "trna", "rrna", "intron", "oril", "orih"]
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	28 #if not $tpe in str($advanced.featuretypes).split(',')
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	29 --$tpe 0
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	30 #end if
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	31 #end for
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	32 --finovl $advanced.finovl
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	33 $advanced.best
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	34 #set fragovl=float($advanced.fragovl)/100.0
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	35 --fragovl $fragovl
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	36 --fragfac $advanced.fragfac
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	37
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	38 --evalue $advanced_prot.evalue
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	39 #set cutoff=float($advanced_prot.cutoff)/100.0
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	40 --cutoff $cutoff
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	41 --clipfac $advanced_prot.clipfac
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	42 $advanced_prot.ncbicode
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	43 $advanced_prot.alarab
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	44 $advanced_prot.oldstst
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	45 $advanced_ncrna.locandgloc
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	46 --ncev $advanced_ncrna.ncev
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	47 $advanced_ncrna.sensitive
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	48 --maxtrnaovl $advanced_ncrna.maxtrnaovl
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	49 --maxrrnaovl $advanced_ncrna.maxrrnaovl
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	50
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	51 #if not ("protein_plot" in str($addoutputs).split(',') or "ncRNA_plot" in str($addoutputs).split(',')):
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	52 --noplots
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	53 #end if
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	54
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	55 #if "raw" in str($addoutputs).split(','):
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	56 && zip -9 -y -r output.zip outdir/ > /dev/null
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	57 #end if
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	58 ]]></command>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	59 <inputs>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	60 <param argument="--input" label="Sequence" type="data" format="fasta" help="a single sequence in fasta formated sequence">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	61 <options options_filter_attribute="metadata.sequences">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	62 <filter type="add_value" value="1"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	63 </options>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	64 </param>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	65 <param argument="--code" label="Genetic code" type="select">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	66 <option value="2">Vertebrate (2)</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	67 <option value="4">Mold, Protozoan, Coelenteral (4)</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	68 <option value="5">Invertebrate (5)</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	69 <option value="9">Echinoderm, Flatworm (9)</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	70 <option value="13">Ascidian (13)</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	71 <option value="14">Alternative Flatworm (14)</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	72 </param>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	73 <param argument="--refseqver" label="Reference data" type="select" help="contact the administrator of this Galaxy instance if you miss reference data">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	74 <options from_data_table="mitos">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	75 <filter type="static_value" value="mitos2" column="2"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	76 </options>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	77 <validator message="No reference annotation is available for MITOS2" type="no_options" />
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	78 </param>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	79 <param argument="--linear" checked="false" label="Treat sequence as linear" type="boolean" truevalue="--linear" falsevalue=""/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	80 <param name="addoutputs" type="select" multiple="true" label="Outputs">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	81 <option value="bed" selected="true">BED</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	82 <option value="mito" selected="false">mito</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	83 <option value="gff" selected="false">GFF file</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	84 <option value="seq" selected="false">SEQ</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	85 <option value="fas" selected="false">nucleotide FASTA</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	86 <option value="faa" selected="false">protein FASTA</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	87 <option value="geneorder" selected="false">geneorder</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	88 <option value="protein_plot" selected="false">Protein prediction plot</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	89 <option value="ncRNA_plot" selected="false">ncRNA prediction plot</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	90 <!--<option value="ncRNA_structure_ps_plots" selected="false">ncRNA structure plots - postscript</option>-->
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	91 <option value="ncRNA_structure_svg_plots" selected="false">ncRNA structure plots - svg</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	92 <option value="raw" selected="false">zipped raw results</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	93 </param>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	94 <section name="advanced" title="Advanced options">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	95 <param name="featuretypes" label="Feature types" help="Feature types that should be predicted by MITOS (--noprot,--notrna,--norrna)" type="select" multiple="true">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	96 <option value="prot" selected="true">Protein coding genes</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	97 <option value="trna" selected="true">tRNAs</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	98 <option value="rrna" selected="true">rRNAs</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	99 <option value="intron" selected="false">Introns</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	100 <option value="oril" selected="false">Origin of light strand replication</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	101 <option value="orih" selected="false">Origin of heavy strand replication</option>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	102 </param>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	103 <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"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	104 <param argument="--best" checked="false" label="Annotate only the best copy of each feature" type="boolean" truevalue="--best" falsevalue=""/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	105 <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"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	106 <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"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	107 </section>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	108 <section name="advanced_prot" title="Advanced options for protein coding gene prediction">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	109 <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"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	110 <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"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	111 <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"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	112 <param argument="--ncbicode" checked="false" label="use start/stop codons as in NCBI (default: learned start/stop codons)" type="boolean" truevalue="--ncbicode" falsevalue=""/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	113 <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=""/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	114 <param argument="--oldstst" checked="false" label="Use the old start/stop prediction method of MITOS1" type="boolean" truevalue="--oldstst" falsevalue=""/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	115 </section>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	116 <section name="advanced_ncrna" title="Advanced options for ncRNA gene prediction">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	117 <param argument="--locandgloc" checked="false" label="Run mitfi in glocal and local mode (default: local only)" type="boolean" truevalue="--locandgloc" falsevalue=""/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	118 <param argument="--ncev" label="e-value to use for inferal fast mode" type="float" min="0" value="0.01"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	119 <param argument="--sensitive" checked="false" label="Use infernals sensitive mode only" type="boolean" truevalue="--sensitive" falsevalue=""/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	120 <param argument="--maxtrnaovl" label="Allow tRNA overlap of up to X nt for mitfi" type="integer" value="50"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	121 <param argument="--maxrrnaovl" label="Allow rRNA overlap of up to X nt for mitfi" type="integer" value="50"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	122 </section>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	123 </inputs>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	124 <outputs>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	125 <data name="bedout" format="bed" from_work_dir="outdir/result.bed">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	126 <filter>"bed" in str(addoutputs)</filter>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	127 </data>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	128 <data name="mitoout" format="tabular" from_work_dir="outdir/result.mitos" label="${tool.name} on ${on_string}: mito">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	129 <filter>"mito" in str(addoutputs)</filter>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	130 </data>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	131 <data name="gffout" format="gff" from_work_dir="outdir/result.gff" label="${tool.name} on ${on_string}: GFF">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	132 <filter>"gff" in str(addoutputs)</filter>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	133 </data>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	134 <data name="seqout" format="txt" from_work_dir="outdir/result.seq" label="${tool.name} on ${on_string}: TBL">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	135 <filter>"seq" in str(addoutputs)</filter>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	136 </data>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	137 <data name="faa" format="fasta" from_work_dir="outdir/result.faa" label="${tool.name} on ${on_string}: aa FASTA">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	138 <filter>"faa" in str(addoutputs)</filter>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	139 </data>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	140 <data name="fas" format="fasta" from_work_dir="outdir/result.fas" label="${tool.name} on ${on_string}: nt FASTA">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	141 <filter>"fas" in str(addoutputs)</filter>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	142 </data>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	143 <data name="geneorderout" format="fasta" from_work_dir="outdir/result.geneorder" label="${tool.name} on ${on_string}: geneorder">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	144 <filter>"geneorder" in str(addoutputs)</filter>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	145 </data>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	146 <data name="protein_plot_out" format="pdf" from_work_dir="outdir/plots/prot.pdf" label="${tool.name} on ${on_string}: Protein prediction plot">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	147 <filter>"protein_plot" in str(addoutputs)</filter>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	148 </data>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	149 <data name="ncRNA_plot_out" format="pdf" from_work_dir="outdir/plots/rna.pdf" label="${tool.name} on ${on_string}: ncRNA prediction plot">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	150 <filter>"ncRNA_plot" in str(addoutputs)</filter>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	151 </data>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	152 <!--<collection name="ncRNA_structure_plot_ps_out" type="list" label="${tool.name} on ${on_string}: ncRNA postscript structure plots">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	153 <discover_datasets pattern="(?P<name>.+)\.ps" format="ps" directory="outdir/plots" />
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	154 <filter>"ncRNA_structure_ps_plots" in str(addoutputs)</filter>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	155 </collection>-->
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	156 <collection name="ncRNA_structure_plot_svg_out" type="list" label="${tool.name} on ${on_string}: ncRNA svg structure plots">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	157 <discover_datasets pattern="(?P<name>.+)\.svg" format="svg" directory="outdir/plots" />
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	158 <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	159 </collection>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	160 <data name="rawout" format="zip" from_work_dir="output.zip" label="${tool.name} on ${on_string}: raw data">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	161 <filter>"raw" in str(addoutputs)</filter>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	162 </data>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	163 </outputs>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	164 <tests>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	165 <!-- default options -->
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	166 <test expect_num_outputs="1">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	167 <param name="input" value="NC_012920.fasta"/>
64e557714a07 "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"/>
64e557714a07 "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" />
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	170 <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	171 <assert_command>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	190 </assert_command>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	191 </test>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	192 <!-- different main options -->
64e557714a07 "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">
64e557714a07 "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"/>
64e557714a07 "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"/>
64e557714a07 "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" />
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	197 <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed" compare="sim_size"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	198 <section name="advanced">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	199 <param name="featuretypes" value="prot,trna,rrna,intron,oril,orih"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	200 <param name="finovl" value="49"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	201 <param name="best" value="true"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	202 <param name="fragovl" value="10"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	203 <param name="fragfac" value="9"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	204 </section>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	205 <assert_command>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	206 <has_text text="--code 5"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	207 <has_text text="--finovl 49"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	208 <not_has_text text="--trna"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	209 <not_has_text text="--rrna"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	210 <not_has_text text="--prot"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	211 <not_has_text text="--intron"/>
64e557714a07 "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="--oril"/>
64e557714a07 "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="--orih"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	214 <has_text text="--evalue 2.0"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	215 <has_text text="--cutoff 0.5"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	216 <has_text text="--clipfac 10.0"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	217 <has_text text="--best"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	218 <has_text text="--fragovl 0.1"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	219 <has_text text="--fragfac 9.0"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	220 <has_text text="--ncev 0.01"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	221 <has_text text="--maxtrnaovl 50"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	222 <has_text text="--maxrrnaovl 50"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	223 <has_text text="--noplots"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	224 </assert_command>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	225 </test>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	226 <!-- different pcg and ncrn options -->
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	227 <test expect_num_outputs="11">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	228 <param name="input" value="NC_012920.fasta"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	229 <param name="code" value="2"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	230 <param name="refseqver" value="mitos2-refdata" />
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	231 <section name="advanced_prot">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	232 <param name="evalue" value="3"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	233 <param name="cutoff" value="49"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	234 <param name="clipfac" value="9"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	235 <param name="ncbicode" value="true"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	236 <param name="alarab" value="true"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	237 <param name="oldstst" value="true"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	238 </section>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	239 <section name="advanced_ncrna">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	240 <!-- <param name="locandgloc" value="true"/> should be possible from 2.0.5 https://gitlab.com/Bernt/MITOS/-/commit/9b4c55c29961c307dce02ac0319dadbd76f6b9e5-->
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	241 <param name="ncev" value="0.1"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	242 <param name="sensitive" value="true"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	243 <param name="maxtrnaovl" value="51"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	244 <param name="maxrrnaovl" value="49"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	245 </section>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	246 <param name="addoutputs" value="bed,mito,gff,seq,fas,faa,geneorder,protein_plot,ncRNA_plot,ncRNA_structure_svg_plots,raw"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	247 <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed" compare="sim_size"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	248 <output name="mitoout" file="mitos2_NC_012920.mitos" ftype="tabular"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	249 <output name="gffout" file="mitos2_NC_012920.gff" ftype="gff"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	250 <output name="seqout" file="mitos2_NC_012920.seq" ftype="txt"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	251 <output name="faa" file="mitos2_NC_012920.faa" ftype="fasta"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	252 <output name="fas" file="mitos2_NC_012920.fas" ftype="fasta"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	253 <output name="geneorderout" file="mitos2_NC_012920.geneorder" ftype="fasta"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	254 <output name="protein_plot_out" file="mitos2_NC_012920_prot.pdf" ftype="pdf" compare="sim_size"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	255 <output name="ncRNA_plot_out" file="mitos2_NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	256 <output name="rawout" ftype="zip">
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	257 <assert_contents>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	258 <has_archive_member path=".*/result.bed"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	259 </assert_contents>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	260 </output>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	261 <output_collection name="ncRNA_structure_plot_svg_out" type="list" count="17"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	262 <assert_command>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	263 <has_text text="--code 2"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	264 <has_text text="--finovl 50"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	265 <not_has_text text="--trna"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	266 <not_has_text text="--rrna"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	267 <not_has_text text="--prot"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	268 <has_text text="--intron 0"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	269 <has_text text="--oril 0"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	270 <has_text text="--orih 0"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	271 <has_text text="--evalue 3.0"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	272 <has_text text="--cutoff 0.49"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	273 <has_text text="--clipfac 9.0"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	274 <has_text text="--alarab"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	275 <has_text text="--oldstst"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	276 <has_text text="--ncbicode"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	277 <not_has_text text="--best"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	278 <has_text text="--fragovl 0.2"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	279 <has_text text="--fragfac 10.0"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	280 <!--<has_text text="\-\-locandgloc"/>-->
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	281 <has_text text="--ncev 0.1"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	282 <has_text text="--sensitive"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	283 <has_text text="--maxtrnaovl 51"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	284 <has_text text="--maxrrnaovl 49"/>
64e557714a07 "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="--noplots"/>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	286 </assert_command>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	287 </test>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	288 </tests>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	289 <help>@COMMON_HELP@
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	290 <![CDATA[
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	291
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	292
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	293 Advanced options
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	294
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	295 - Feature types
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	296
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	297 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.
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	298
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	299 - Final overlap (nt)
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	300
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	301 Maximum number of nucleotides by which genes of different types may overlap. Applies to merging of the final predictions.
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	302
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	303 - Annotate only the best copy of each feature
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	304
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	305 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)
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	306
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	307 - Fragment overlap
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	308
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	309 Maximum fraction (of the shorter feature) allowed that two hits overlap in the query to be counted as fragments.
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	310
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	311 - Fragment quality factor
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	312
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	313 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.
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	314
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	315 Advanced options for protein coding gene prediction
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	316
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	317 - BLAST E-value Exponent
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	318
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	319 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).
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	320
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	321 - Quality cutoff
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	322
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	323 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
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	324
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	325 - Clipping factor
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	326
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	327 Clipping is started if overlapping prediction of hits with the same name differ by less than a factor X in their quality value.
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	328
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	329 - use start/stop codons as in NCBI (default: learned start/stop codons)
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	330
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	331 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)
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	332
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	333 - Use the hmmer based method of Al Arab et al. 2016. This will consider the evalue, ncbicode, fragovl, fragfac parameters
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	334
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	335 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.
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	336
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	337 - Use the old start/stop prediction method of MITOS1
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	338
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	339 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)
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	340
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	341 Advanced options for ncRNA gene prediction
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	342
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	343 - Run mitfi in glocal and local mode (default: local only)
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	344
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	345 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.
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	346
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	347 - e-value to use for inferal fast mode
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	348
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	349 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.
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	350
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	351 - Use infernal's sensitive mode only
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	352
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	353 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.
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	354
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	355 - Allow tRNA/rRNA overlap of up to X nt for mitfi
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	356
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	357 Allow that a tRNA/rRNA overlaps with another feature by this number of nucleotides.
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	358
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	359 ]]></help>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	360 <citations>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	361 <citation type="doi">10.1093/nar/gkz833</citation>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	362 <citation type="doi">10.1016/j.ympev.2016.09.024</citation>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	363 </citations>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	364 </tool>
64e557714a07 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" iuc parents: diff changeset	365

Mercurial > repos > iuc > mitos2

annotate mitos2.xml @ 3:994e1ce9f4d5 draft