mitos2: mitos2.xml comparison

comparison mitos2.xml @ 3:624606f7c996 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit f23e76fe2b03f7c5f66e0609a6cf3c96beaed0c4

author	iuc
date	Tue, 14 Jun 2022 17:16:16 +0000
parents	80323066acd4
children	033755194fe9

comparison

equal deleted inserted replaced

-:80323066acd4
+:624606f7c996
 <tool id="mitos2" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
 <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@">MITOS2</token>
 <token name="@TOOL_VERSION@">2.0.6</token>
-<token name="@VERSION_SUFFIX@">1</token>
+<token name="@VERSION_SUFFIX@">2</token>
 </macros>
 <requirements>
 <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
-<requirement type="package">zip</requirement>
+<requirement type="package" version="3.0">zip</requirement>
 </requirements>
 <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
 <command detect_errors="aggressive"><![CDATA[
 mkdir outdir &&
 --ncev $advanced_ncrna.ncev
 $advanced_ncrna.sensitive
 --maxtrnaovl $advanced_ncrna.maxtrnaovl
 --maxrrnaovl $advanced_ncrna.maxrrnaovl
-#if not ("protein_plot" in str($addoutputs).split(',') or "ncRNA_plot" in str($addoutputs).split(',')):
+#if not ("protein_plot" in $addoutputs or "ncRNA_plot" in $addoutputs):
 --noplots
+#end if
+#if "missing" in $addoutputs:
+> outdir/missing.txt
 #end if
 #if "raw" in str($addoutputs).split(','):
 && zip -9 -y -r output.zip outdir/ > /dev/null
 #end if
 ]]></command>
 <inputs>
-<param argument="--input" label="Sequence" type="data" format="fasta" help="a single sequence in fasta formated sequence">
+<param argument="--input" label="Sequence" type="data" format="fasta" help="A single sequence in fasta formated sequence">
 <options options_filter_attribute="metadata.sequences">
 <filter type="add_value" value="1"/>
 </options>
 </param>
 <param argument="--code" label="Genetic code" type="select">
 <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="--refseqver" label="Reference data" type="select" help="contact the administrator of this Galaxy instance if you miss reference data">
+<param argument="--refseqver" 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="mitos2" column="2"/>
 </options>
 <validator message="No reference annotation is available for MITOS2" type="no_options" />
 </param>
 <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>
+<option value="missing" selected="false">Missing genes</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>
 </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="1"/>
 <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="--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="--ncbicode" checked="false" label="use start/stop codons as in NCBI (default: learned start/stop codons)" type="boolean" truevalue="--ncbicode" falsevalue=""/>
+<param argument="--ncbicode" checked="false" label="Use start/stop codons as in NCBI (default: learned start/stop codons)" type="boolean" truevalue="--ncbicode" falsevalue=""/>
 <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=""/>
 <param argument="--oldstst" checked="false" label="Use the old start/stop prediction method of MITOS1" type="boolean" truevalue="--oldstst" falsevalue=""/>
 </section>
 <section name="advanced_ncrna" title="Advanced options for ncRNA gene prediction">
 <param argument="--locandgloc" checked="false" label="Run mitfi in glocal and local mode (default: local only)" type="boolean" truevalue="--locandgloc" falsevalue=""/>
 <discover_datasets pattern="(?P&lt;name&gt;.+)\.svg" format="svg" directory="outdir/plots" />
 <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter>
 </collection>
 <data name="rawout" format="zip" from_work_dir="output.zip" label="${tool.name} on ${on_string}: raw data">
 <filter>"raw" in str(addoutputs)</filter>
+</data>
+<data name="missing_genes" format="txt" from_work_dir="outdir/missing.txt" label="${tool.name} on ${on_string}: missing genes">
+<filter>"missing" in str(addoutputs)</filter>
 </data>
 </outputs>
 <tests>
 <!-- default options -->
 <test expect_num_outputs="1">
 <has_text text="--maxtrnaovl 51"/>
 <has_text text="--maxrrnaovl 49"/>
 <not_has_text text="--noplots"/>
 </assert_command>
 </test>
+<!-- missing genes -->
+<test expect_num_outputs="2">
+<param name="input" value="NC_012920.fasta"/>
+<param name="code" value="2"/>
+<param name="refseqver" value="mitos2-refdata" />
+<param name="addoutputs" value="bed,missing"/>
+<output name="bedout" file="mitos2_NC_012920.bed" ftype="bed"/>
+<output name="missing_genes" file="missing_genes.txt" ftype="txt"/>
+<assert_command>
+<has_text text="--code 2"/>
+<has_text text="--finovl 50"/>
+<not_has_text text="--trna"/>
+<not_has_text text="--rrna"/>
+<not_has_text text="--prot"/>
+<has_text text="--intron 0"/>
+<has_text text="--oril 0"/>
+<has_text text="--orih 0"/>
+<has_text text="--evalue 2.0"/>
+<has_text text="--cutoff 0.5"/>
+<has_text text="--clipfac 10.0"/>
+<not_has_text text="--best"/>
+<has_text text="--fragovl 0.2"/>
+<has_text text="--fragfac 10.0"/>
+<has_text text="--ncev 0.01"/>
+<has_text text="--maxtrnaovl 50"/>
+<has_text text="--maxrrnaovl 50"/>
+<has_text text="--noplots"/>
+</assert_command>
+</test>
 </tests>
 <help>@COMMON_HELP@
 <![CDATA[
 - Use infernal's sensitive mode only
 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.
 - Allow tRNA/rRNA overlap of up to X nt for mitfi
 Allow that a tRNA/rRNA overlaps with another feature by this number of nucleotides.
 ]]></help>
 <citations>

Mercurial > repos > iuc > mitos2

comparison mitos2.xml @ 3:624606f7c996 draft