/
mitos.xml
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mitos.xml
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<tool id="mitos" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
<description>de-novo annotation of metazoan mitochondrial genomes</description>
<xrefs>
<xref type='bio.tools'>mitos</xref>
</xrefs>
<macros>
<import>macros.xml</import>
<token name="@MITOS_NAME@">MITOS</token>
<token name="@TOOL_VERSION@">1.1.1</token>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
</requirements>
<version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
<command detect_errors="aggressive"><![CDATA[
mkdir outdir &&
runmitos.py
--input '$input'
--code $code
--outdir outdir
--refdir '$refdir.fields.path'
#for tpe in ["prot", "trna", "rrna"]
#if not $tpe in str($advanced.featuretypes).split(',')
--no$tpe
#end if
#end for
--finovl $advanced.finovl
--evalue $advanced_prot.evalue
--cutoff $advanced_prot.cutoff
#set maxovl=float($advanced_prot.maxovl)/100.0
--maxovl $maxovl
--clipfac $advanced_prot.clipfac
#set fragovl=float($advanced_prot.fragovl)/100.0
--fragovl $fragovl
--fragfac $advanced_prot.fragfac
--ststrange $advanced_prot.ststrange
#if "raw" in str($addoutputs).split(','):
--zip
#end if
]]></command>
<inputs>
<param argument="--input" label="sequence" type="data" format="fasta" help="a single sequence in fasta formated sequence">
<validator type="dataset_metadata_in_range" metadata_name="sequences" min="1" max="1"/>
</param>
<param argument="--code" label="Genetic code" type="select">
<option value="2">Vertebrate (2)</option>
<option value="4">Mold, Protozoan, Coelenteral (4)</option>
<option value="5">Invertebrate (5)</option>
<option value="9">Echinoderm, Flatworm (9)</option>
<option value="13">Ascidian (13)</option>
<option value="14">Alternative Flatworm (14)</option>
</param>
<param argument="--refdir" label="Reference data" type="select" help="contact the administrator of this Galaxy instance if you miss reference data">
<options from_data_table="mitos">
<filter type="static_value" value="mitos" column="2"/>
</options>
<validator message="No reference annotation is available for MITOS" type="no_options" />
</param>
<param name="addoutputs" type="select" multiple="true" label="Outputs">
<option value="bed" selected="true">BED</option>
<option value="mito" selected="false">mito</option>
<option value="gff" selected="false">GFF file</option>
<option value="seq" selected="false">SEQ</option>
<option value="fas" selected="false">nucleotide FASTA</option>
<option value="faa" selected="false">protein FASTA</option>
<option value="geneorder" selected="false">geneorder</option>
<option value="protein_plot" selected="false">Protein prediction plot</option>
<option value="ncRNA_plot" selected="false">ncRNA prediction plot</option>
<!--<option value="ncRNA_structure_ps_plots" selected="false">ncRNA structure plots - postscript</option>-->
<option value="ncRNA_structure_svg_plots" selected="false">ncRNA structure plots - svg</option>
<option value="raw" selected="false">zipped raw results</option>
</param>
<section name="advanced" title="Advanced options">
<param name="featuretypes" label="Feature types" help="Feature types that should be predicted by MITOS (--noprot,--notrna,--norrna)" type="select" multiple="true">
<option value="prot" selected="true">Protein coding genes</option>
<option value="trna" selected="true">tRNAs</option>
<option value="rrna" selected="true">rRNAs</option>
</param>
<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"/>
</section>
<section name="advanced_prot" title="Advanced options for protein coding gene prediction">
<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
<param argument="--ststrange" label="Start/stop range" help="Number of aminoacids searched for start and stop codon of proteins" type="integer" value="6"/>
</section>
</inputs>
<outputs>
<data name="bedout" format="bed" from_work_dir="outdir/result.bed">
<filter>"bed" in str(addoutputs)</filter>
</data>
<data name="mitoout" format="tabular" from_work_dir="outdir/result" label="${tool.name} on ${on_string}: mito">
<filter>"mito" in str(addoutputs)</filter>
</data>
<data name="gffout" format="gff" from_work_dir="outdir/result.gff" label="${tool.name} on ${on_string}: GFF">
<filter>"gff" in str(addoutputs)</filter>
</data>
<data name="seqout" format="txt" from_work_dir="outdir/result.seq" label="${tool.name} on ${on_string}: TBL">
<filter>"seq" in str(addoutputs)</filter>
</data>
<data name="fasout" format="fasta" from_work_dir="outdir/result.fas" label="${tool.name} on ${on_string}: nt FASTA">
<filter>"fas" in str(addoutputs)</filter>
</data>
<data name="faaout" format="fasta" from_work_dir="outdir/result.faa" label="${tool.name} on ${on_string}: aa FASTA">
<filter>"faa" in str(addoutputs)</filter>
</data>
<data name="geneorderout" format="fasta" from_work_dir="outdir/result.geneorder" label="${tool.name} on ${on_string}: geneorder">
<filter>"geneorder" in str(addoutputs)</filter>
</data>
<data name="protein_plot_out" format="pdf" from_work_dir="outdir/plots/prot.pdf" label="${tool.name} on ${on_string}: Protein prediction plot">
<filter>"protein_plot" in str(addoutputs)</filter>
</data>
<data name="ncRNA_plot_out" format="pdf" from_work_dir="outdir/plots/rna.pdf" label="${tool.name} on ${on_string}: ncRNA prediction plot">
<filter>"protein_plot" in str(addoutputs)</filter>
</data>
<collection name="ncRNA_structure_plot_svg_out" type="list" label="${tool.name} on ${on_string}: ncRNA svg structure plots">
<discover_datasets pattern="(?P<name>.+)\.svg" format="svg" directory="outdir/plots" />
<filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter>
</collection>
<data name="rawout" format="zip" from_work_dir="outdir.zip" label="${tool.name} on ${on_string}: raw data">
<filter>"raw" in str(addoutputs)</filter>
</data>
</outputs>
<tests>
<!-- default options -->
<test expect_num_outputs="1">
<param name="input" value="NC_012920.fasta"/>
<param name="code" value="2"/>
<param name="refdir" value="mitos1-refdata" />
<output name="bedout" file="NC_012920.bed" ftype="bed"/>
<assert_command>
<has_text text="--code 2"/>
<has_text text="--finovl 35"/>
<has_text text="--evalue 2.0"/>
<has_text text="--cutoff 50"/>
<has_text text="--maxovl 0.2"/>
<has_text text="--clipfac 10.0"/>
<has_text text="--fragovl 0.2"/>
<has_text text="--fragfac 10.0"/>
<has_text text="--ststrange 6"/>
</assert_command>
</test>
<!-- default options, add outputs -->
<test expect_num_outputs="11">
<param name="input" value="NC_012920.fasta"/>
<param name="code" value="2"/>
<param name="refdir" value="mitos1-refdata" />
<param name="addoutputs" value="bed,mito,gff,seq,fas,faa,raw,geneorder,protein_plot,ncRNA_plot,ncRNA_structure_svg_plots"/>
<output name="bedout" file="NC_012920.bed" ftype="bed"/>
<output name="mitoout" file="NC_012920.mito" ftype="tabular" />
<output name="gffout" file="NC_012920.gff" ftype="gff" />
<output name="seqout" file="NC_012920.seq" ftype="txt" />
<output name="fasout" file="NC_012920.fas" ftype="fasta" />
<output name="faaout" file="NC_012920.faa" ftype="fasta" />
<output name="rawout" ftype="zip">
<assert_contents>
<has_archive_member path="result.bed"/>
</assert_contents>
</output>
<output name="geneorderout" file="NC_012920.geneorder" ftype="fasta" />
<output name="protein_plot_out" file="NC_012920_prot.pdf" ftype="pdf" compare="sim_size"/>
<output name="ncRNA_plot_out" file="NC_012920_ncrna.pdf" ftype="pdf" compare="sim_size"/>
<output_collection name="ncRNA_structure_plot_svg_out" type="list" count="24">
<element name="trnA-5586-5654" file="NC_012920_trnA.svg" ftype="svg" />
</output_collection>
<assert_command>
<has_text text="--code 2"/>
<has_text text="--finovl 35"/>
<has_text text="--evalue 2.0"/>
<has_text text="--cutoff 50"/>
<has_text text="--maxovl 0.2"/>
<has_text text="--clipfac 10.0"/>
<has_text text="--fragovl 0.2"/>
<has_text text="--fragfac 10.0"/>
<has_text text="--ststrange 6"/>
</assert_command>
</test>
<!-- no rRNA, and advanced options -->
<test expect_num_outputs="1">
<param name="input" value="NC_012920.fasta"/>
<param name="code" value="2"/>
<param name="refdir" value="mitos1-refdata" />
<param name="advanced|featuretypes" value="prot,trna" />
<param name="advanced|finovl" value="50" />
<output name="bedout" file="NC_012920.bed" ftype="bed" compare="sim_size"/>
<assert_command>
<has_text text="--code 2"/>
<has_text text="--norrna"/>
<has_text text="--finovl 50"/>
</assert_command>
</test>
<!-- no rRNA, no tRNA; advanced protein options -->
<test expect_num_outputs="1">
<param name="input" value="NC_012920.fasta"/>
<param name="code" value="5"/>
<param name="refdir" value="mitos1-refdata" />
<param name="advanced|featuretypes" value="prot" />
<param name="advanced_prot|evalue" value="3"/>
<param name="advanced_prot|cutoff" value="40"/>
<param name="advanced_prot|maxovl" value="30"/>
<param name="advanced_prot|clipfac" value="5"/>
<param name="advanced_prot|fragovl" value="15"/>
<param name="advanced_prot|fragfac" value="11"/>
<param name="advanced_prot|ststrange" value="12"/>
<param name="addoutputs" value="bed"/>
<output name="bedout" file="NC_012920.bed" ftype="bed" compare="sim_size"/>
<assert_command>
<has_text text="--code 5"/>
<has_text text="--evalue 3"/>
<has_text text="--cutoff 40"/>
<has_text text="--maxovl 0.3"/>
<has_text text="--clipfac 5.0"/>
<has_text text="--fragovl 0.15"/>
<has_text text="--fragfac 11.0"/>
<has_text text="--ststrange 12"/>
</assert_command>
</test>
</tests>
<help>
@COMMON_HELP@
<![CDATA[
]]></help>
<citations>
<citation type="doi">10.1016/j.ympev.2012.08.023</citation>
</citations>
</tool>