| Previous changeset 4:79f2d2f0ca2c (2025-07-14) Next changeset 6:ce6377ab5aca (2025-09-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit e21d81020b381293e58e72ad54b782ce4a30ab56 |
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modified:
macros.xml ppanggolin_all.xml |
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added:
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 |
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| diff -r 79f2d2f0ca2c -r d2b0073ef8d6 macros.xml --- a/macros.xml Mon Jul 14 07:48:53 2025 +0000 +++ b/macros.xml Thu Aug 14 17:09:17 2025 +0000 |
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| @@ -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> |
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| diff -r 79f2d2f0ca2c -r d2b0073ef8d6 ppanggolin_all.xml --- a/ppanggolin_all.xml Mon Jul 14 07:48:53 2025 +0000 +++ b/ppanggolin_all.xml Thu Aug 14 17:09:17 2025 +0000 |
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| b'@@ -7,27 +7,12 @@\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+ #import re\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+ mkdir -p ./tmp_ppanggolin/all &&\n+ mkdir -p ./tmp_ppanggolin/organism_list &&\n+ \n+ @ORGANISM_LIST@\n \n ppanggolin all\n \n@@ -36,11 +21,12 @@\n #elif $extension_input_files == "genbank":\n --anno\n #end if\n- "./tmp_ppanggolin/organism_list/organism.list"\n+ ./tmp_ppanggolin/organism_list/organism.list\n \n- -o ./tmp_ppanggolin/all\n+ --output ./tmp_ppanggolin/all\n --force\n --cpu "\\${GALAXY_SLOTS:-4}"\n+ --disable_prog_bar\n \n --coverage $coverage\n --identity $identity\n@@ -53,6 +39,11 @@\n \n $do_defrag\n \n+ \n+ && ppanggolin info\n+ --pangenome ./tmp_ppanggolin/all/pangenome.h5\n+ > ./tmp_ppanggolin/all/ppanggolin_info.txt\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@@ -85,7 +76,7 @@\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+ #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@@ -112,7 +103,7 @@\n \t\t&& cat ./tmp_ppanggolin/all/gene_presence_absence.Rtab > \'${gene_presence_absence}\'\n #end if\n \n- \n+ && cat ./tmp_ppanggolin/all/ppanggolin_info.txt > \'${ppanggolin_info}\'\n && cat ./tmp_ppanggolin/all/regions_of_genomic_plasticity.tsv > \'${regions_of_genomic_plasticity}\'\n && cat ./tmp_ppanggolin/all/pangenome.h5 > \'${pangenome_h5}\'\n && cat ./tmp_ppanggolin/all/genomes_statistics.tsv > \'${genomes_statistics}\'\n@@ -121,49 +112,15 @@\n ]]></command>\n \n <inputs>\n- \n- <param name="genomes" type="data" multiple="true" min="2" label="Select genome files" format="fasta,genbank" help="All the genome files must be of similar format, either all genbank files or all fasta files. Processing of at least 15 genomes files is recommended, a minimum of 2 genomes files is mandatory. Space is not allowed in filename.">\n- </param>\n \n- <param argument="--identity" type="float" value="0.8" min="0" max="1" label="Minimum alignment identity"/>\n- <param argument="--coverage" type="float" value="0.8" min="0" max="1" label="Minimum alignment coverage"/>\n+ <expand macro="inputs_genomes" min="2" extratexthelp=" Processing of at least 15 genomes files is recommended." />\n+ \n+ <expand macro="inputs_identity_coverage_do_defrag"/>\n \n- <param argument="--nb_of_partitions" type="integer" max="20" label="Number of classes used to partition the pangenome" optional="true" help="If emp'..b've Yeast Nuclear</option>\n- <option value="13">13 - Ascidian Mitochondrial</option>\n- <option value="14">14 - Flatworm Mitochondrial</option>\n- <option value="15">15 - Blepharisma Nuclear</option>\n- <option value="16">16 - Chlorophycean Mitochondrial</option>\n- <option value="21">21 - Trematode Mitochondrial</option>\n- <option value="22">22 - Scenedesmus obliquus Mitochondrial</option>\n- <option value="23">23 - Thraustochytrium Mitochondrial</option>\n- <option value="24">24 - Pterobranchia Mitochondrial</option>\n- <option value="25">25 - Candidate Division SR1 and Gracilibacteria</option>\n- <option value="26">26 - Pachysolen tannophilus Nuclear</option>\n- <option value="27">27 - Karyorelict Nuclear</option>\n- <option value="28">28 - Condylostoma Nuclear</option>\n- <option value="29">29 - Mesodinium Nuclear</option>\n- <option value="30">30 - Peritrich Nuclear</option>\n- <option value="31">31 - Blastocrithidia Nuclear</option>\n- <option value="32">32 - Balanophoraceae Plastid</option>\n- <option value="33">33 - Cephalodiscidae Mitochondrial</option>\n- </param>\n- <param name="do_defrag" type="boolean" checked="true" label="Gene family defragmentation" truevalue="" falsevalue="--no_defrag"/>\n+ <expand macro="inputs_nb_of_partitions"/>\n \n-\n+ <expand macro="inputs_translation_table"/>\n+ \n <param name="advanced_pangenome_optional_files" type="select" label="Add the following pangenome output files in the Galaxy history" multiple="true" optional="true" display="checkboxes" >\n \t<!-- Basic files -->\n <option value="output_gene_presence_absence" selected="true">Gene presence absence</option>\n@@ -252,7 +209,7 @@\n <filter>advanced_pangenome_optional_files and "output_gene_presence_absence" in advanced_pangenome_optional_files</filter>\n </data>\n \n- \n+ <data name="ppanggolin_info" format="txt" label="PPanGGOLiN all on ${on_string}: PPanGGOLiN info" />\n <data 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@@ -260,7 +217,7 @@\n </outputs>\n \n <tests>\n- <test expect_num_outputs="21">\n+ <test expect_num_outputs="22">\n <param name="nb_of_partitions" value="3"/>\n <param name="coverage" value="0.8"/>\n <param name="identity" value="0.8"/>\n@@ -277,8 +234,18 @@\n <has_text text="region" />\n </assert_contents>\n </output>\n+ <output name="ppanggolin_info" >\n+ <assert_contents>\n+ <has_text text="Content:" />\n+ </assert_contents>\n+ </output>\n+ <output name="Ushaped_plot" >\n+ <assert_contents>\n+ <has_text text="html" />\n+ </assert_contents>\n+ </output>\n </test>\n- <test expect_num_outputs="21">\n+ <test expect_num_outputs="22">\n <param name="nb_of_partitions" value="3"/>\n <param name="coverage" value="0.8"/>\n <param name="identity" value="0.8"/>\n@@ -295,6 +262,11 @@\n <has_text text="region" />\n </assert_contents>\n </output>\n+ <output name="ppanggolin_info" >\n+ <assert_contents>\n+ <has_text text="Content:" />\n+ </assert_contents>\n+ </output>\n </test>\n <test expect_failure="true">\n <param name="nb_of_partitions" value="3"/>\n' |
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