Mercurial > repos > iuc > ppanggolin_msa
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit 6f13ba99c86ba17b6a83baedf328e04190cec247
author | iuc |
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date | Tue, 16 Sep 2025 13:11:57 +0000 |
parents | e331e475e854 |
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<macros> <token name="@TOOL_VERSION@">2.2.5</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="citation"> <citations> <citation type="doi">10.1371/journal.pcbi.1007732</citation> <citation type="doi">10.1093/bioinformatics/btaa792</citation> </citations> </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">ppanggolin</requirement> </requirements> </xml> <xml name="xrefs"> <xrefs> <xref type="bio.tools">ppanggolin</xref> </xrefs> </xml> <token name="@ORGANISM_LIST@"><![CDATA[ touch ./tmp_ppanggolin/organism_list/organism.list && #set extension_input_files = "" #for $counter_input_files, $file in enumerate($genomes): #if $counter_input_files == 0: #set extension_input_files = $file.ext #else: #if $file.ext != $extension_input_files: #raise Exception("All the genome files must be of the same datatype, either all genbank files or all fasta files.") #end if #end if #set base_name = re.sub('[^\w\-_\.]', '_', str($file.element_identifier)) echo -e '${base_name}\t${file}' >> ./tmp_ppanggolin/organism_list/organism.list && #end for ]]></token> <xml name="inputs_identity_coverage_do_defrag"> <param argument="--identity" type="float" value="0.8" min="0" max="1" label="Minimum alignment identity"/> <param argument="--coverage" type="float" value="0.8" min="0" max="1" label="Minimum alignment coverage"/> <param name="do_defrag" type="boolean" checked="true" label="Gene family defragmentation" truevalue="" falsevalue="--no_defrag" help="Realign gene families to link fragments with their non-fragmented gene family. (--no_defrag)"/> </xml> <xml name="inputs_nb_of_partitions"> <param argument="--nb_of_partitions" type="integer" max="20" label="Number of classes used to partition the pangenome" optional="true" help="If empty value (default), it will be automatically determined. Otherwise, the value needs to be between 2 and 20 and it is advised to set a value of 3. See the link for the documentation in the help section for more details."> <validator type="expression" message="Value needs to be empty or an integer between 2 and 20">value == "" or int(value) >= 2</validator> </param> </xml> <xml name="inputs_translation_table"> <param argument="--translation_table" type="select" label="Translation table"> <option value="1" selected="true">1 - Standard Code</option> <option value="2">2 - Vertebrate Mitochondrial</option> <option value="3">3 - Yeast Mitochondrial</option> <option value="4">4 - Mold, Protozoan, and Coelenterate Mitochondrial</option> <option value="5">5 - Invertebrate Mitochondrial</option> <option value="6">6 - Ciliate Nuclear</option> <option value="9">9 - Echinoderm Mitochondrial</option> <option value="10">10 - Euplotid Nuclear</option> <option value="11">11 - Bacterial and Plant Plastid</option> <option value="12">12 - Alternative Yeast Nuclear</option> <option value="13">13 - Ascidian Mitochondrial</option> <option value="14">14 - Flatworm Mitochondrial</option> <option value="15">15 - Blepharisma Nuclear</option> <option value="16">16 - Chlorophycean Mitochondrial</option> <option value="21">21 - Trematode Mitochondrial</option> <option value="22">22 - Scenedesmus obliquus Mitochondrial</option> <option value="23">23 - Thraustochytrium Mitochondrial</option> <option value="24">24 - Pterobranchia Mitochondrial</option> <option value="25">25 - Candidate Division SR1 and Gracilibacteria</option> <option value="26">26 - Pachysolen tannophilus Nuclear</option> <option value="27">27 - Karyorelict Nuclear</option> <option value="28">28 - Condylostoma Nuclear</option> <option value="29">29 - Mesodinium Nuclear</option> <option value="30">30 - Peritrich Nuclear</option> <option value="31">31 - Blastocrithidia Nuclear</option> <option value="32">32 - Balanophoraceae Plastid</option> <option value="33">33 - Cephalodiscidae Mitochondrial</option> </param> </xml> <xml name="inputs_pangenome"> <param argument="--pangenome" name="pangenome_h5" type="data" format="h5" label="Input pangenome h5 file"/> </xml> <xml name="inputs_soft_core"> <param argument="--soft_core" type="float" value="0.95" min="0" max="1" label="Soft core threshold used when generating general statistics on the projected genome" help="Default=0.95 .This threshold does not influence PPanGGOLiN's partitioning. The value determines the minimum fraction of genomes that must possess a gene family for it to be considered part of the soft core."/> </xml> <xml name="inputs_genomes" token_min="1" token_extratexthelp=""> <param name="genomes" type="data" multiple="true" min="@MIN@" label="Genome files" format="fasta,genbank" help="All the genome files must be of the same format, either all genbank files or all fasta files. A minimum of @MIN@ genome file(s) is mandatory.@EXTRATEXTHELP@ Special characters and spaces are replaced by underscore."/> </xml> </macros>