| Next changeset 1:a83148dac159 (2025-02-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3 |
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added:
macros.xml ppanggolin_all.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 |
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| diff -r 000000000000 -r 6fdee3720de7 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jan 22 10:34:50 2025 +0000 |
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| @@ -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> |
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| diff -r 000000000000 -r 6fdee3720de7 ppanggolin_all.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ppanggolin_all.xml Wed Jan 22 10:34:50 2025 +0000 |
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| b'@@ -0,0 +1,324 @@\n+<tool id="ppanggolin_all" name="PPanGGOLiN all" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">\n+ <description>generates a partitioned pangenome</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="xrefs"/>\n+ <expand macro="requirements"/>\n+\n+ <command detect_errors="exit_code"><![CDATA[\n+ \n+ mkdir -p "./tmp_ppanggolin/all" &&\n+ mkdir -p "./tmp_ppanggolin/organism_list" &&\n+ mkdir -p "./tmp_ppanggolin/ln_input_genomes" &&\n+ \n+ touch "./tmp_ppanggolin/organism_list/organism.list" &&\n+ \n+ #set extension_input_files = ""\n+ #for $counter_input_files, $file in enumerate($genomes):\n+ #if $counter_input_files == 0:\n+ \t#set extension_input_files = $file.ext\n+ #else:\n+ #if $file.ext != $extension_input_files:\n+ #raise Exception("All the genome files must be of the same datatype, either all genbank files or all fasta files.")\n+ \t#end if\n+ #end if\n+ \n+ #set base_name = str($file.element_identifier).replace(" ", "_")\n+ echo -e \'${base_name}\\t${file}\' >> "./tmp_ppanggolin/organism_list/organism.list" &&\n+ \n+ #end for\n+\n+ ppanggolin all\n+\n+ #if $extension_input_files == "fasta":\n+ --fasta\n+ #elif $extension_input_files == "genbank":\n+ --anno\n+ #end if\n+ "./tmp_ppanggolin/organism_list/organism.list"\n+ \n+ -o ./tmp_ppanggolin/all\n+ --force\n+ --cpu "\\${GALAXY_SLOTS:-4}"\n+ \n+ --coverage $coverage\n+ --identity $identity\n+ --translation_table $translation_table\n+ \n+ \n+ #if str($nb_of_partitions) != "":\n+ --nb_of_partitions $nb_of_partitions\n+ #end if\n+ \n+ $do_defrag\n+ \n+\n+ #if "output_functional_modules" in $advanced_pangenome_optional_files:\n+\t\t&& cat ./tmp_ppanggolin/all/functional_modules.tsv > \'${functional_modules}\'\n+ #end if\n+ #if "output_modules_RGP_lists" in $advanced_pangenome_optional_files:\n+\t\t&& cat ./tmp_ppanggolin/all/modules_RGP_lists.tsv > \'${modules_RGP_lists}\'\n+ #end if\n+ #if "output_modules_spots" in $advanced_pangenome_optional_files:\n+\t\t&& cat ./tmp_ppanggolin/all/modules_spots.tsv > \'${modules_spots}\'\n+ #end if\n+ #if "output_modules_in_genomes" in $advanced_pangenome_optional_files:\n+\t\t&& cat ./tmp_ppanggolin/all/modules_in_genomes.tsv > \'${modules_in_genomes}\'\n+ #end if\n+ #if "output_modules_summary" in $advanced_pangenome_optional_files:\n+\t\t&& cat ./tmp_ppanggolin/all/modules_summary.tsv > \'${modules_summary}\'\n+ #end if\n+ #if "output_spot_borders" in $advanced_pangenome_optional_files:\n+\t\t&& cat ./tmp_ppanggolin/all/spot_borders.tsv > \'${spot_borders}\'\n+ #end if\n+ #if "output_spots" in $advanced_pangenome_optional_files:\n+\t\t&& cat ./tmp_ppanggolin/all/spots.tsv > \'${spots}\'\n+ #end if\n+ #if "output_summarize_spots" in $advanced_pangenome_optional_files:\n+\t\t&& cat ./tmp_ppanggolin/all/summarize_spots.tsv > \'${summarize_spots}\'\n+ #end if\n+ #if "output_border_protein_genes" in $advanced_pangenome_optional_files:\n+\t\t&& cat ./tmp_ppanggolin/all/border_protein_genes.fasta > \'${border_protein_genes}\'\n+ #end if\n+ \n+ #if "output_tile_plot" in $advanced_pangenome_optional_files:\n+ \t&& cat ./tmp_ppanggolin/all/tile_plot.html > \'${tile_plot}\'\n+ #end if\n+ #if "output_ushaped_plot" in $advanced_pangenome_optional_files:\n+ \t&& cat ./tmp_ppanggolin/all/Ushaped_plot.html > \'${Ushaped_plot}\'\n+ #end if\n+ \n+ #if "output_pangenomeGraph_json" in $advanced_pangenome_optional_files:\n+ && cat ./tmp_ppanggolin/all/pangenomeGraph.json > \'${pangenomeGraph_json}\'\n+ #end if\n+ #if "out'..b'ata name="regions_of_genomic_plasticity" format="tsv" label="PPanGGOLiN all on ${on_string}: Regions of genomic plasticity" />\n+ <data name="pangenome_h5" format="h5" label="PPanGGOLiN all on ${on_string}: PanGenome HDF5 file" />\n+ <data name="genomes_statistics" format="tsv" label="PPanGGOLiN all on ${on_string}: Genome statistics" />\n+ \n+ </outputs>\n+\n+ <tests>\n+ <test expect_num_outputs="21">\n+ <param name="nb_of_partitions" value="3"/>\n+ <param name="coverage" value="0.8"/>\n+ <param name="identity" value="0.8"/>\n+ <param name="translation_table" value="1"/>\n+ <param name="genomes" value="fasta/AP028611_984801_1194801.fasta.gz,fasta/CP107038_1022972_1232972.fasta.gz,fasta/CP113115_1290693_1440693.fasta.gz,fasta/LN831051_1254175_1464175.fasta.gz,fasta/NC_012467_959209_1169209.fasta.gz" ftype="fasta"/>\n+ <output name="genomes_statistics" >\n+ <assert_contents>\n+ <has_text text="#soft_core=" />\n+ <has_text text="#duplication_margin=" />\n+ </assert_contents>\n+ </output>\n+ <output name="regions_of_genomic_plasticity" >\n+ <assert_contents>\n+ <has_text text="region" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="21">\n+ <param name="nb_of_partitions" value="3"/>\n+ <param name="coverage" value="0.8"/>\n+ <param name="identity" value="0.8"/>\n+ <param name="translation_table" value="1"/>\n+ <param name="genomes" value="genbank/AP028611_984801_1194801.gb.gz,genbank/CP107038_1022972_1232972.gb.gz,genbank/CP113115_1290693_1440693.gb.gz,genbank/LN831051_1254175_1464175.gb.gz,genbank/NC_012467_959209_1169209.gb.gz" ftype="genbank"/>\n+ <output name="genomes_statistics" >\n+ <assert_contents>\n+ <has_text text="#soft_core=" />\n+ <has_text text="#duplication_margin=" />\n+ </assert_contents>\n+ </output>\n+ <output name="regions_of_genomic_plasticity" >\n+ <assert_contents>\n+ <has_text text="region" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_failure="true">\n+ <param name="nb_of_partitions" value="3"/>\n+ <param name="coverage" value="0.8"/>\n+ <param name="identity" value="0.8"/>\n+ <param name="translation_table" value="1"/>\n+ <param name="genomes" value="genbank/AP028611_984801_1194801.gb.gz,genbank/CP107038_1022972_1232972.gb.gz,genbank/CP113115_1290693_1440693.gb.gz,fasta/AP028611_984801_1194801.fasta.gz,fasta/CP107038_1022972_1232972.fasta.gz,fasta/CP113115_1290693_1440693.fasta.gz" ftype="genbank"/>\n+ </test>\n+ </tests>\n+ \n+ <help><![CDATA[\n+ \n+ PPanGGOLiN_ (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either assembled \n+ genomic DNA sequences or provided genome annotations. PPanGGOLiN builds pangenomes through a graphical model and a statistical method to partition gene \n+ families in persistent, shell and cloud genomes. It integrates both information on protein-coding genes and their genomic neighborhood to build a graph \n+ of gene families where each node is a gene family, and each edge is a relation of genetic contiguity. \n+\n+\tThe `ppanggolin all` command generates a partitioned pangenome graph with predicted RGP, spots and modules. Please see the documentation_ on how parameters can be tuned for this command.\n+\n+ .. _PPanGGOLiN: https://github.com/labgem/PPanGGOLiN\n+ .. _documentation: https://ppanggolin.readthedocs.io/en/latest/user/QuickUsage/quickAnalyses.html\n+ \n+ ]]></help>\n+\n+ <expand macro="citation"/>\n+ \n+</tool>\n' |
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