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comparison mitos2.xml @ 3:624606f7c996 draft

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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
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2:80323066acd4 3:624606f7c996
1 <tool id="mitos2" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="mitos2" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>de-novo annotation of metazoan mitochondrial genomes</description> 2 <description>de-novo annotation of metazoan mitochondrial genomes</description>
3 <xrefs>
4 <xref type='bio.tools'>mitos</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <import>macros.xml</import> 7 <import>macros.xml</import>
5 <token name="@MITOS_NAME@">MITOS2</token> 8 <token name="@MITOS_NAME@">MITOS2</token>
6 <token name="@TOOL_VERSION@">2.0.6</token> 9 <token name="@TOOL_VERSION@">2.0.6</token>
7 <token name="@VERSION_SUFFIX@">1</token> 10 <token name="@VERSION_SUFFIX@">2</token>
8 </macros> 11 </macros>
9 <requirements> 12 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">mitos</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
11 <requirement type="package">zip</requirement> 14 <requirement type="package" version="3.0">zip</requirement>
12 </requirements> 15 </requirements>
13 <version_command>python -c "import mitos; print(mitos.__version__)"</version_command> 16 <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
14 <command detect_errors="aggressive"><![CDATA[ 17 <command detect_errors="aggressive"><![CDATA[
15 mkdir outdir && 18 mkdir outdir &&
16 19
43 --ncev $advanced_ncrna.ncev 46 --ncev $advanced_ncrna.ncev
44 $advanced_ncrna.sensitive 47 $advanced_ncrna.sensitive
45 --maxtrnaovl $advanced_ncrna.maxtrnaovl 48 --maxtrnaovl $advanced_ncrna.maxtrnaovl
46 --maxrrnaovl $advanced_ncrna.maxrrnaovl 49 --maxrrnaovl $advanced_ncrna.maxrrnaovl
47 50
48 #if not ("protein_plot" in str($addoutputs).split(',') or "ncRNA_plot" in str($addoutputs).split(',')): 51 #if not ("protein_plot" in $addoutputs or "ncRNA_plot" in $addoutputs):
49 --noplots 52 --noplots
53 #end if
54
55 #if "missing" in $addoutputs:
56 > outdir/missing.txt
50 #end if 57 #end if
51 58
52 #if "raw" in str($addoutputs).split(','): 59 #if "raw" in str($addoutputs).split(','):
53 && zip -9 -y -r output.zip outdir/ > /dev/null 60 && zip -9 -y -r output.zip outdir/ > /dev/null
54 #end if 61 #end if
55 ]]></command> 62 ]]></command>
56 <inputs> 63 <inputs>
57 <param argument="--input" label="Sequence" type="data" format="fasta" help="a single sequence in fasta formated sequence"> 64 <param argument="--input" label="Sequence" type="data" format="fasta" help="A single sequence in fasta formated sequence">
58 <options options_filter_attribute="metadata.sequences"> 65 <options options_filter_attribute="metadata.sequences">
59 <filter type="add_value" value="1"/> 66 <filter type="add_value" value="1"/>
60 </options> 67 </options>
61 </param> 68 </param>
62 <param argument="--code" label="Genetic code" type="select"> 69 <param argument="--code" label="Genetic code" type="select">
65 <option value="5">Invertebrate (5)</option> 72 <option value="5">Invertebrate (5)</option>
66 <option value="9">Echinoderm, Flatworm (9)</option> 73 <option value="9">Echinoderm, Flatworm (9)</option>
67 <option value="13">Ascidian (13)</option> 74 <option value="13">Ascidian (13)</option>
68 <option value="14">Alternative Flatworm (14)</option> 75 <option value="14">Alternative Flatworm (14)</option>
69 </param> 76 </param>
70 <param argument="--refseqver" label="Reference data" type="select" help="contact the administrator of this Galaxy instance if you miss reference data"> 77 <param argument="--refseqver" label="Reference data" type="select" help="Contact the administrator of this Galaxy instance if you miss reference data">
71 <options from_data_table="mitos"> 78 <options from_data_table="mitos">
72 <filter type="static_value" value="mitos2" column="2"/> 79 <filter type="static_value" value="mitos2" column="2"/>
73 </options> 80 </options>
74 <validator message="No reference annotation is available for MITOS2" type="no_options" /> 81 <validator message="No reference annotation is available for MITOS2" type="no_options" />
75 </param> 82 </param>
85 <option value="protein_plot" selected="false">Protein prediction plot</option> 92 <option value="protein_plot" selected="false">Protein prediction plot</option>
86 <option value="ncRNA_plot" selected="false">ncRNA prediction plot</option> 93 <option value="ncRNA_plot" selected="false">ncRNA prediction plot</option>
87 <!--<option value="ncRNA_structure_ps_plots" selected="false">ncRNA structure plots - postscript</option>--> 94 <!--<option value="ncRNA_structure_ps_plots" selected="false">ncRNA structure plots - postscript</option>-->
88 <option value="ncRNA_structure_svg_plots" selected="false">ncRNA structure plots - svg</option> 95 <option value="ncRNA_structure_svg_plots" selected="false">ncRNA structure plots - svg</option>
89 <option value="raw" selected="false">zipped raw results</option> 96 <option value="raw" selected="false">zipped raw results</option>
97 <option value="missing" selected="false">Missing genes</option>
90 </param> 98 </param>
91 <section name="advanced" title="Advanced options"> 99 <section name="advanced" title="Advanced options">
92 <param name="featuretypes" label="Feature types" help="Feature types that should be predicted by MITOS (--noprot,--notrna,--norrna)" type="select" multiple="true"> 100 <param name="featuretypes" label="Feature types" help="Feature types that should be predicted by MITOS (--noprot,--notrna,--norrna)" type="select" multiple="true">
93 <option value="prot" selected="true">Protein coding genes</option> 101 <option value="prot" selected="true">Protein coding genes</option>
94 <option value="trna" selected="true">tRNAs</option> 102 <option value="trna" selected="true">tRNAs</option>
104 </section> 112 </section>
105 <section name="advanced_prot" title="Advanced options for protein coding gene prediction"> 113 <section name="advanced_prot" title="Advanced options for protein coding gene prediction">
106 <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"/> 114 <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"/>
107 <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"/> 115 <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"/>
108 <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"/> 116 <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"/>
109 <param argument="--ncbicode" checked="false" label="use start/stop codons as in NCBI (default: learned start/stop codons)" type="boolean" truevalue="--ncbicode" falsevalue=""/> 117 <param argument="--ncbicode" checked="false" label="Use start/stop codons as in NCBI (default: learned start/stop codons)" type="boolean" truevalue="--ncbicode" falsevalue=""/>
110 <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=""/> 118 <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=""/>
111 <param argument="--oldstst" checked="false" label="Use the old start/stop prediction method of MITOS1" type="boolean" truevalue="--oldstst" falsevalue=""/> 119 <param argument="--oldstst" checked="false" label="Use the old start/stop prediction method of MITOS1" type="boolean" truevalue="--oldstst" falsevalue=""/>
112 </section> 120 </section>
113 <section name="advanced_ncrna" title="Advanced options for ncRNA gene prediction"> 121 <section name="advanced_ncrna" title="Advanced options for ncRNA gene prediction">
114 <param argument="--locandgloc" checked="false" label="Run mitfi in glocal and local mode (default: local only)" type="boolean" truevalue="--locandgloc" falsevalue=""/> 122 <param argument="--locandgloc" checked="false" label="Run mitfi in glocal and local mode (default: local only)" type="boolean" truevalue="--locandgloc" falsevalue=""/>
154 <discover_datasets pattern="(?P&lt;name&gt;.+)\.svg" format="svg" directory="outdir/plots" /> 162 <discover_datasets pattern="(?P&lt;name&gt;.+)\.svg" format="svg" directory="outdir/plots" />
155 <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter> 163 <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter>
156 </collection> 164 </collection>
157 <data name="rawout" format="zip" from_work_dir="output.zip" label="${tool.name} on ${on_string}: raw data"> 165 <data name="rawout" format="zip" from_work_dir="output.zip" label="${tool.name} on ${on_string}: raw data">
158 <filter>"raw" in str(addoutputs)</filter> 166 <filter>"raw" in str(addoutputs)</filter>
167 </data>
168 <data name="missing_genes" format="txt" from_work_dir="outdir/missing.txt" label="${tool.name} on ${on_string}: missing genes">
169 <filter>"missing" in str(addoutputs)</filter>
159 </data> 170 </data>
160 </outputs> 171 </outputs>
161 <tests> 172 <tests>
162 <!-- default options --> 173 <!-- default options -->
163 <test expect_num_outputs="1"> 174 <test expect_num_outputs="1">
280 <has_text text="--maxtrnaovl 51"/> 291 <has_text text="--maxtrnaovl 51"/>
281 <has_text text="--maxrrnaovl 49"/> 292 <has_text text="--maxrrnaovl 49"/>
282 <not_has_text text="--noplots"/> 293 <not_has_text text="--noplots"/>
283 </assert_command> 294 </assert_command>
284 </test> 295 </test>
296 <!-- missing genes -->
297 <test expect_num_outputs="2">
298 <param name="input" value="NC_012920.fasta"/>
299 <param name="code" value="2"/>
300 <param name="refseqver" value="mitos2-refdata" />
301 <param name="addoutputs" value="bed,missing"/>
302 <output name="bedout" file="mitos2_NC_012920.bed" ftype="bed"/>
303 <output name="missing_genes" file="missing_genes.txt" ftype="txt"/>
304 <assert_command>
305 <has_text text="--code 2"/>
306 <has_text text="--finovl 50"/>
307 <not_has_text text="--trna"/>
308 <not_has_text text="--rrna"/>
309 <not_has_text text="--prot"/>
310 <has_text text="--intron 0"/>
311 <has_text text="--oril 0"/>
312 <has_text text="--orih 0"/>
313 <has_text text="--evalue 2.0"/>
314 <has_text text="--cutoff 0.5"/>
315 <has_text text="--clipfac 10.0"/>
316 <not_has_text text="--best"/>
317 <has_text text="--fragovl 0.2"/>
318 <has_text text="--fragfac 10.0"/>
319 <has_text text="--ncev 0.01"/>
320 <has_text text="--maxtrnaovl 50"/>
321 <has_text text="--maxrrnaovl 50"/>
322 <has_text text="--noplots"/>
323 </assert_command>
324 </test>
285 </tests> 325 </tests>
286 <help>@COMMON_HELP@ 326 <help>@COMMON_HELP@
287 <![CDATA[ 327 <![CDATA[
288 328
289 329
347 387
348 - Use infernal's sensitive mode only 388 - Use infernal's sensitive mode only
349 389
350 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. 390 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.
351 391
352 - Allow tRNA/rRNA overlap of up to X nt for mitfi 392 - Allow tRNA/rRNA overlap of up to X nt for mitfi
353 393
354 Allow that a tRNA/rRNA overlaps with another feature by this number of nucleotides. 394 Allow that a tRNA/rRNA overlaps with another feature by this number of nucleotides.
355 395
356 ]]></help> 396 ]]></help>
357 <citations> 397 <citations>