Mercurial > repos > iuc > ppanggolin_msa
changeset 0:d305623d5f41 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3
| author | iuc |
|---|---|
| date | Wed, 22 Jan 2025 10:34:36 +0000 |
| parents | |
| children | 76170454dc91 |
| files | macros.xml ppanggolin_msa.xml test-data/fasta/AP028611_984801_1194801.fasta.gz test-data/fasta/CP107038_1022972_1232972.fasta.gz test-data/fasta/CP113115_1290693_1440693.fasta.gz test-data/fasta/LN831051_1254175_1464175.fasta.gz test-data/fasta/NC_012467_959209_1169209.fasta.gz test-data/genbank/AP028611_984801_1194801.gb.gz test-data/genbank/CP107038_1022972_1232972.gb.gz test-data/genbank/CP113115_1290693_1440693.gb.gz test-data/genbank/LN831051_1254175_1464175.gb.gz test-data/genbank/NC_012467_959209_1169209.gb.gz test-data/h5/test_data.h5 |
| diffstat | 13 files changed, 174 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jan 22 10:34:36 2025 +0000 @@ -0,0 +1,19 @@ +<macros> + <token name="@TOOL_VERSION@">2.2.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="citation"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1007732</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> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ppanggolin_msa.xml Wed Jan 22 10:34:36 2025 +0000 @@ -0,0 +1,155 @@ +<tool id="ppanggolin_msa" name="PPanGGOLiN MSA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> + <description>computes MSA of pangenome's gene families</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="xrefs"/> + <expand macro="requirements"/> + + <command detect_errors="exit_code"><![CDATA[ + + mkdir -p "./tmp_ppanggolin/msa" && + mkdir -p "./tmp_ppanggolin/tmpdir_msa" && + + ppanggolin msa + --pangenome '$pangenome_h5' + --output ./tmp_ppanggolin/msa + --tmpdir ./tmp_ppanggolin/tmpdir_msa + --force + --cpu "\${GALAXY_SLOTS:-4}" + --disable_prog_bar + --partition $choice_partition + #if str($input_choose_partition.choice_partition) == "softcore" + --soft_core $choice_soft_core + #end if + + --source $choice_source + $do_phylo + $do_single_copy + --translation_table $translation_table + + #set base_msa_source = "msa_" + str($input_choose_partition.choice_partition) + "_" + str($choice_source) + #set base_genome_alignment = str($input_choose_partition.choice_partition) + "_genome_alignment.aln" + #if str($input_choose_partition.choice_partition) == "softcore" + #set base_genome_alignment = str($input_choose_partition.choice_partition) + "_" + str($choice_soft_core) + "_genome_alignment.aln" + #end if + + && tar -cvf ./tmp_ppanggolin/msa/archive_${base_msa_source}.tar ./tmp_ppanggolin/msa/${base_msa_source} + && gzip ./tmp_ppanggolin/msa/archive_${base_msa_source}.tar + && mv ./tmp_ppanggolin/msa/archive_${base_msa_source}.tar.gz '${archive_msa_partition_source}' + + #if str($do_phylo) == "--phylo" + && mv ./tmp_ppanggolin/msa/${base_genome_alignment} '${partition_genome_alignment}' + #end if + + ]]></command> + + <inputs> + + <param argument="--pangenome" name="pangenome_h5" type="data" format="h5" label="Input pangenome h5 file"/> + + <conditional name="input_choose_partition"> + <param argument="--partition" name="choice_partition" type="select" label="Partition"> + <option value="core" selected="true">Core</option> + <option value="persistent">Persistent</option> + <option value="shell">Shell</option> + <option value="cloud">Cloud</option> + <option value="softcore">Softcore</option> + <option value="accessory">Accessory</option> + <option value="all">All</option> + </param> + <when value="core"/> + <when value="persistent"/> + <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"/> + </when> + <when value="accessory"/> + <when value="all"/> + </conditional> + + <param argument="--source" name="choice_source" type="select" label="Source"> + <option value="protein" selected="true">Protein</option> + <option value="dna">DNA</option> + </param> + + <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> + + </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" > + <filter>do_phylo is True</filter> + </data> + </outputs> + + <tests> + <test expect_num_outputs="2"> + <param name="choice_partition" value="core"/> + <param name="choice_source" value="protein"/> + <param name="do_phylo" value="true"/> + <param name="do_single_copy" value="false"/> + <param name="pangenome_h5" value="h5/test_data.h5" ftype="h5"/> + <param name="translation_table" value="1"/> + + <output name="partition_genome_alignment" > + <assert_contents> + <has_text text=">" /> + </assert_contents> + </output> + + </test> + </tests> + + <help><![CDATA[ + + PPanGGOLiN_ (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either assembled + genomic DNA sequences or provided genome annotations. PPanGGOLiN builds pangenomes through a graphical model and a statistical method to partition gene + families in persistent, shell and cloud genomes. It integrates both information on protein-coding genes and their genomic neighborhood to build a graph + of gene families where each node is a gene family, and each edge is a relation of genetic contiguity. + + The `ppanggolin msa` command computes multiple sequence alignment of any partition of the pangenome. The command uses mafft with default options to perform the alignment. Please see the documentation_ on how parameters can be tuned for this command. + + .. _PPanGGOLiN: https://github.com/labgem/PPanGGOLiN + .. _documentation: https://ppanggolin.readthedocs.io/en/latest/user/MSA.html + + ]]></help> + + <expand macro="citation"/> + +</tool> +