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comparison mitos2.xml @ 6:6cd432abcf8e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos commit 24a59e271fbe0b87d826d1d36b3a9ea008227adc
author iuc
date Wed, 10 Dec 2025 23:30:17 +0000
parents c8f5229645ef
children
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5:c8f5229645ef 6:6cd432abcf8e
1 <tool id="mitos2" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 1 <tool id="mitos2" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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>
6 <macros> 3 <macros>
7 <import>macros.xml</import> 4 <import>macros.xml</import>
8 <token name="@MITOS_NAME@">MITOS2</token> 5 <token name="@MITOS_NAME@">MITOS2</token>
9 <token name="@TOOL_VERSION@">2.1.3</token> 6 <token name="@TOOL_VERSION@">2.1.10</token>
10 <token name="@VERSION_SUFFIX@">0</token> 7 <token name="@VERSION_SUFFIX@">0</token>
11 </macros> 8 </macros>
9 <xrefs>
10 <xref type="bio.tools">mitos</xref>
11 </xrefs>
12 <requirements> 12 <requirements>
13 <requirement type="package" version="@TOOL_VERSION@">mitos</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">mitos</requirement>
14 </requirements> 14 </requirements>
15 <version_command>python -c "import mitos; print(mitos.__version__)"</version_command> 15 <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>
16 <command detect_errors="aggressive"><![CDATA[ 16 <command detect_errors="aggressive"><![CDATA[
17 mkdir outdir && 17 mkdir outdir &&
18 18
19 runmitos.py 19 runmitos
20 --input '$input' 20 --input '$input'
21 --code $code 21 --code $code
22 --outdir outdir 22 --outdir outdir
23 --refdir '/' 23 --refdir '/'
24 --refseqver '$refseqver.fields.path' 24 --refseqver '$refseqver.fields.path'
45 --ncev $advanced_ncrna.ncev 45 --ncev $advanced_ncrna.ncev
46 $advanced_ncrna.sensitive 46 $advanced_ncrna.sensitive
47 --maxtrnaovl $advanced_ncrna.maxtrnaovl 47 --maxtrnaovl $advanced_ncrna.maxtrnaovl
48 --maxrrnaovl $advanced_ncrna.maxrrnaovl 48 --maxrrnaovl $advanced_ncrna.maxrrnaovl
49 49
50 #if not ("protein_plot" in $addoutputs or "ncRNA_plot" in $addoutputs): 50 #if not ("protein_plot" in $addoutputs or "ncRNA_plot" in $addoutputs or "ncRNA_structure_svg_plots" in $addoutputs):
51 --noplots 51 --noplots
52 #end if 52 #end if
53 #if "raw" in str($addoutputs).split(','): 53 #if "raw" in str($addoutputs).split(','):
54 --zip 54 --zip
55 #end if 55 #end if
62 <param argument="--input" label="Sequence" type="data" format="fasta" help="A single sequence in fasta formated sequence"> 62 <param argument="--input" label="Sequence" type="data" format="fasta" help="A single sequence in fasta formated sequence">
63 <validator type="dataset_metadata_in_range" metadata_name="sequences" min="1" max="1"/> 63 <validator type="dataset_metadata_in_range" metadata_name="sequences" min="1" max="1"/>
64 </param> 64 </param>
65 <param argument="--code" label="Genetic code" type="select"> 65 <param argument="--code" label="Genetic code" type="select">
66 <option value="2">Vertebrate (2)</option> 66 <option value="2">Vertebrate (2)</option>
67 <option value="3">Yeast (3)</option>
67 <option value="4">Mold, Protozoan, Coelenteral (4)</option> 68 <option value="4">Mold, Protozoan, Coelenteral (4)</option>
68 <option value="5">Invertebrate (5)</option> 69 <option value="5">Invertebrate (5)</option>
69 <option value="9">Echinoderm, Flatworm (9)</option> 70 <option value="9">Echinoderm, Flatworm (9)</option>
70 <option value="13">Ascidian (13)</option> 71 <option value="13">Ascidian (13)</option>
71 <option value="14">Alternative Flatworm (14)</option> 72 <option value="14">Alternative Flatworm (14)</option>
73 <option value="21">Trematode (21)</option>
74 <option value="24">Rhabdopleuridae (24)</option>
75 <option value="33">Cephalodiscidae (33)</option>
72 </param> 76 </param>
73 <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">
74 <options from_data_table="mitos"> 78 <options from_data_table="mitos">
75 <filter type="static_value" value="mitos2" column="2"/> 79 <filter type="static_value" value="mitos2" column="2"/>
76 </options> 80 </options>
292 <has_text text="--maxrrnaovl 49"/> 296 <has_text text="--maxrrnaovl 49"/>
293 <not_has_text text="--noplots"/> 297 <not_has_text text="--noplots"/>
294 </assert_command> 298 </assert_command>
295 </test> 299 </test>
296 <!-- missing genes --> 300 <!-- missing genes -->
297 <test expect_num_outputs="2"> 301 <test expect_num_outputs="3">
298 <param name="input" value="NC_012920.fasta"/> 302 <param name="input" value="NC_012920.fasta"/>
299 <param name="code" value="2"/> 303 <param name="code" value="2"/>
300 <param name="refseqver" value="mitos2-refdata" /> 304 <param name="refseqver" value="mitos2-refdata" />
301 <param name="addoutputs" value="bed,missing"/> 305 <param name="addoutputs" value="bed,missing,ncRNA_structure_svg_plots"/>
302 <output name="bedout" file="mitos2_NC_012920.bed" compare="re_match" ftype="bed"/> 306 <output name="bedout" file="mitos2_NC_012920.bed" compare="re_match" ftype="bed"/>
303 <output name="missing_genes" ftype="txt"> 307 <output name="missing_genes" ftype="txt">
304 <assert_contents> 308 <assert_contents>
305 <has_size value="167"/> 309 <has_size value="167"/>
306 </assert_contents> 310 </assert_contents>
307 </output> 311 </output>
312 <output_collection name="ncRNA_structure_plot_svg_out" type="list" count="5"/>
308 <assert_command> 313 <assert_command>
309 <has_text text="--code 2"/> 314 <has_text text="--code 2"/>
310 <has_text text="--finovl 50"/> 315 <has_text text="--finovl 50"/>
311 <not_has_text text="--trna"/> 316 <not_has_text text="--trna"/>
312 <not_has_text text="--rrna"/> 317 <not_has_text text="--rrna"/>
321 <has_text text="--fragovl 0.2"/> 326 <has_text text="--fragovl 0.2"/>
322 <has_text text="--fragfac 10.0"/> 327 <has_text text="--fragfac 10.0"/>
323 <has_text text="--ncev 0.01"/> 328 <has_text text="--ncev 0.01"/>
324 <has_text text="--maxtrnaovl 50"/> 329 <has_text text="--maxtrnaovl 50"/>
325 <has_text text="--maxrrnaovl 50"/> 330 <has_text text="--maxrrnaovl 50"/>
326 <has_text text="--noplots"/> 331 <has_text text="--noplots" negate="true"/>
327 </assert_command> 332 </assert_command>
328 </test> 333 </test>
329 </tests> 334 </tests>
330 <help>@COMMON_HELP@ 335 <help>@COMMON_HELP@
331 <![CDATA[ 336 <![CDATA[