Mercurial > repos > iuc > ppanggolin_msa
changeset 5:e331e475e854 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56
| author | iuc |
|---|---|
| date | Thu, 14 Aug 2025 17:09:07 +0000 |
| parents | 7a09c51a14be |
| children | |
| files | macros.xml ppanggolin_msa.xml test-data/fasta/PROJECT1_984801_1194801.fasta.gz test-data/fasta/PROJECT5_1290693_1440693.fasta.gz test-data/fasta/PROJECT8_1022972_1232972.fasta.gz test-data/genbank/PROJECT1_984801_1194801.gb.gz test-data/genbank/PROJECT5_1290693_1440693.gb.gz test-data/genbank/PROJECT8_1022972_1232972.gb.gz |
| diffstat | 8 files changed, 74 insertions(+), 36 deletions(-) [+] |
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--- a/macros.xml Mon Jul 14 07:49:02 2025 +0000 +++ b/macros.xml Thu Aug 14 17:09:07 2025 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.2.4</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="citation"> <citations> <citation type="doi">10.1371/journal.pcbi.1007732</citation> @@ -17,4 +17,70 @@ <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>
--- a/ppanggolin_msa.xml Mon Jul 14 07:49:02 2025 +0000 +++ b/ppanggolin_msa.xml Thu Aug 14 17:09:07 2025 +0000 @@ -8,8 +8,8 @@ <command detect_errors="exit_code"><![CDATA[ - mkdir -p "./tmp_ppanggolin/msa" && - mkdir -p "./tmp_ppanggolin/tmpdir_msa" && + mkdir -p ./tmp_ppanggolin/msa && + mkdir -p ./tmp_ppanggolin/tmpdir_msa && ppanggolin msa --pangenome '$pangenome_h5' @@ -46,7 +46,7 @@ <inputs> - <param argument="--pangenome" name="pangenome_h5" type="data" format="h5" label="Input pangenome h5 file"/> + <expand macro="inputs_pangenome"/> <conditional name="input_choose_partition"> <param argument="--partition" name="choice_partition" type="select" label="Partition"> @@ -63,7 +63,7 @@ <when value="shell"/> <when value="cloud"/> <when value="softcore"> - <param argument="--soft_core" name="choice_soft_core" type="float" value="0.95" min="0" max="1" label="Soft core threshold to use if 'softcore' partition is chosen"/> + <expand macro="inputs_soft_core"/> </when> <when value="accessory"/> <when value="all"/> @@ -77,42 +77,14 @@ <param argument="--phylo" name="do_phylo" type="boolean" checked="true" label="Writes a whole genome msa file for additional phylogenetic analysis (recommended)" truevalue="--phylo" falsevalue=""/> <param argument="--single_copy" name="do_single_copy" type="boolean" checked="false" label="Report gene families that are considered 'single copy'" truevalue="--single_copy" falsevalue=""/> - - <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> + + <expand macro="inputs_translation_table"/> </inputs> <outputs> <data name="archive_msa_partition_source" format="tar.gz" label="PPanGGOLiN msa on ${on_string}: archive msa ${choice_partition} ${choice_source}" /> - <data name="partition_genome_alignment" format="aln" label="PPanGGOLiN msa on ${on_string}: ${choice_partition} genome alignment" > + <data name="partition_genome_alignment" format="maf" label="PPanGGOLiN msa on ${on_string}: ${choice_partition} genome alignment" > <filter>do_phylo is True</filter> </data> </outputs>