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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta commit 6adea21f21f7445e92568579096b7c7ea4781e50
| author | iuc |
|---|---|
| date | Wed, 22 Oct 2025 15:47:16 +0000 |
| parents | 137d00a9a598 |
| children |
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<tool id="panta" name="PanTA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> <description>Efficient inference of large prokaryotic pangenomes with PanTA</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ mkdir out && #import re, os #set input_directory = 'input_directory' mkdir $input_directory && #if $input_type.input_type_selector == "gff": #for gff in $input_type.input_gff #set $filename = '%s.gff' % re.sub('[^\w_-]', '_', str($gff.element_identifier)) cp '$gff' '$input_directory/$filename' && #end for #elif $input_type.input_type_selector == "tsv": #set $filename = '%s.tsv' % re.sub('[^\w_-]', '_', str($input_type.input_tsv.element_identifier)) cp '$input_type.input_tsv' '$input_directory/$filename' && #end if #if $mode.select_mode == "main": panta main #if $input_type.input_type_selector == "gff": -g $input_directory/*.gff #elif $input_type.input_type_selector == "tsv": -f $input_directory/*.tsv #end if -o out $dont_split --blast '$blast' --identity '$identity' --LD '$LD' --AL '$AL' --AS '$AS' --evalue '$evalue' --threads "\${GALAXY_SLOTS:-8}" --table '$table' #if $alignment != 'None': --alignment '$alignment' #end if && tar -czf collection_dir.tar.gz -C out . #elif $mode.select_mode == "add": mkdir -p extracted_dir && ln -s $collection_dir collection_dir.tar.gz && tar --strip-components=1 -xzf collection_dir.tar.gz -C extracted_dir && panta add #if $input_type.input_type_selector == "gff": -g $input_directory/*.gff #elif $input_type.input_type_selector == "tsv": -f $input_directory/*.tsv #end if -c extracted_dir $dont_split --blast '$blast' --identity '$identity' --LD '$LD' --AL '$AL' --AS '$AS' --evalue '$evalue' --threads "\${GALAXY_SLOTS:-8}" --table '$table' #if $alignment != 'None': --alignment '$alignment' #end if && cp -r extracted_dir/* out #end if ]]></command> <inputs> <conditional name="mode"> <param label="Select mode" name="select_mode" type="select"> <option selected="true" value="main">Use PanTA main</option> <option value="add">Use PanTA add</option> </param> <when value="main"/> <when value="add"> <param name="collection_dir" type="data" format="tar,tar.gz" label="Previous collection directory"/> </when> </conditional> <conditional name="input_type"> <param name="input_type_selector" type="select" label="Choose the input format"> <option value="gff" selected="true">GFF File</option> <option value="tsv">TSV File</option> </param> <when value="gff"> <param type="data_collection" name="input_gff" format="gff3" collection_type="list" label="Select input files to analyze" help="Select the files you wish to analyze with PanTA"/> </when> <when value="tsv"> <param type="data" name="input_tsv" format="tsv,tabular" multiple="false" label="Select input file to analyze" help="Select the file you wish to analyze with PanTA"/> </when> </conditional> <param argument="--dont-split" type="boolean" truevalue="--dont-split" falsevalue="" label="Dont split" help="Decide for or against splitting paralog clusters"/> <param argument="--blast" type="select" label="Alignment method" help="Method for all-against-all alignment (default: diamond)"> <option value="diamond" selected="True">Diamond</option> <option value="blast">Blast</option> </param> <param argument="--identity" type="float" value="0.7" label="Minimum percentage identity" help="Set the minimum percentage identity"/> <param argument="--LD" type="float" value="0.7" label="Length difference cutoff" help="Set the length difference cutoff between two sequences"/> <param argument="--AL" type="float" value="0" label="Alignment coverage for the longer sequence" help="Set the alignment coverage for the longer sequence"/> <param argument="--AS" type="float" value="0" label="Alignment coverage for the shorter sequence" help="Set the alignment coverage for the shorter sequence"/> <param argument="--evalue" type="float" value="1e-06" label="Blast evalue" help="Maximum expected value for reporting hits and lower values are stricter"/> <param argument="--table" type="integer" value="" label="Codon table" help="Set the codon table"/> <param argument="--alignment" type="select" label="Run alignment for each gene cluster"> <option value="None" selected="True">None</option> <option value="nucleotide">Nucleotide</option> <option value="protein">Protein</option> </param> </inputs> <outputs> <!--Basic PanTA main outputs --> <data format="json" name="annotated_clusters" label="${tool.name} on ${on_string} : Annotated Clusters" from_work_dir="out/annotated_clusters.json"/> <data format="tsv" name="blast_output" label="${tool.name} on ${on_string} : BLAST" from_work_dir="out/blast.tsv"/> <data format="json" name="clusters" label="${tool.name} on ${on_string} : Clusters" from_work_dir="out/clusters.json"/> <data format="csv" name="gene_annotation" label="${tool.name} on ${on_string} : Gene Annotation" from_work_dir="out/gene_annotation.csv"/> <data format="csv" name="gene_position" label="${tool.name} on ${on_string} : Gene Position" from_work_dir="out/gene_position.csv"/> <data format="csv" name="gene_presence_absence" label="${tool.name} on ${on_string} : Gene Presence Absence" from_work_dir="out/gene_presence_absence.csv"/> <data format="txt" name="gene_presence_absence_Rtab" label="${tool.name} on ${on_string} : Gene Presence Absence Rtab" from_work_dir="out/gene_presence_absence.Rtab"/> <data format="fasta" name="representative_clusters_nucl" label="${tool.name} on ${on_string} : Representative Clusters Nucl" from_work_dir="out/representative_clusters_nucl.fasta"/> <data format="fasta" name="representative_clusters_prot" label="${tool.name} on ${on_string} : Representative Clusters Prot" from_work_dir="out/representative_clusters_prot.fasta"/> <data format="fasta" name="representative" label="${tool.name} on ${on_string} : Representative FASTA" from_work_dir="out/representative.fasta"/> <data format="json" name="samples" label="${tool.name} on ${on_string} : Samples" from_work_dir="out/samples.json"/> <data format="txt" name="summary_statistics" label="${tool.name} on ${on_string} : Summary Statistics" from_work_dir="out/summary_statistics.txt"/> <!--Alignment outputs --> <data format="fasta" name="core_gene_alignment" label="${tool.name} on ${on_string} : Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln.gz"> <filter> ['alignment'] != 'None' </filter> </data> <data format="fasta" name="pan_genome_reference" label="${tool.name} on ${on_string} : Pan Genome Reference" from_work_dir="out/pan_genome_reference.fna"> <filter> ['alignment'] != 'None' </filter> </data> </outputs> <tests> <!--Test 01: Basic PanTA main test for gff files: Tests the basic command for PanTA main --> <test expect_num_outputs="14"> <conditional name="mode"> <param name="select_mode" value="main"/> </conditional> <conditional name="input_type"> <param name="input_type_selector" value="gff"/> <param name="input_gff"> <collection type="list"> <element name="GCA_021342655.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021342655.1.gff"/> <element name="GCA_021534865.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021534865.1.gff"/> <element name="GCA_021697815.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021697815.1.gff"/> <element name="GCA_021890555.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021890555.1.gff"/> </collection> </param> </conditional> <param name="table" value="10"/> <output name="annotated_clusters" ftype="json"> <assert_contents> <has_text text="GCA_021342655.1-NZ_JAJTPH010000093.1-5475-cds-WP_000557454.1"/> <has_n_lines n="96508" delta='3'/> </assert_contents> </output> <output name="blast_output" ftype="tsv"> <assert_contents> <has_text text="GCA_021342655.1-NZ_JAJTPH010000101.1-3-cds-WP_233337042.1"/> <has_n_lines n="30680" delta='3'/> </assert_contents> </output> <output name="clusters" ftype="json"> <assert_contents> <has_text text="GCA_021890555.1-NZ_JAKLOD010000002.1-4878-cds-L3T02_RS24235"/> <has_n_lines n="24266" delta='3'/> </assert_contents> </output> <output name="gene_annotation" ftype="csv"> <assert_contents> <has_text text="IclR family transcriptional regulator,6"/> <has_n_lines n="19712" delta='3'/> </assert_contents> </output> <output name="gene_position" ftype="csv"> <assert_contents> <has_text text="1-NZ_JAJTPH010000010.1-23-cds-LXO36_RS13380"/> <has_n_lines n="195" delta='3'/> </assert_contents> </output> <output name="gene_presence_absence" ftype="csv"> <assert_contents> <has_n_lines n="7682" delta='3'/> </assert_contents> </output> <output name="gene_presence_absence_Rtab" ftype="txt"> <assert_contents> <has_n_lines n="7682" delta='3'/> </assert_contents> </output> <output name="representative_clusters_nucl" ftype="fasta"> <assert_contents> <has_text text="GGTCTGCCCCACCGGCATCGACATTCGCGACGGCCTGCAGATCGAGTGCATTGGTTGCGC"/> <has_n_lines n="124180" delta='3'/> </assert_contents> </output> <output name="representative_clusters_prot" ftype="fasta"> <assert_contents> <has_text text="GLPHRHRHSRRPADRVHWLRRLHRCLRQHHGQDGLPQGPDQLHNRTQSFRTEDPSAAPTP"/> <has_n_lines n="49014" delta='3'/> </assert_contents> </output> <output name="representative" ftype="fasta"> <assert_contents> <has_text text="RIEGSVWPKSIRGSTPKVRGTCQIERAASESPHFMRFHVACPHCGEEQYLKFGDKETPFGLKWTPDDPSSVFYLCEHNACVIRQQELDFTDARYICEKTGIWTRDGILWFSSSGEEIEPPDSVTFHIWTAYSPFTTWVQIVKDWMKTKGDTGKRKTFVNTTLGETWEAKIGERPDAEVMAERKEHYSAPVPDRVAYLTAGIDSQLDRYEMRVWGWGPGEESWLIDRQIIMGRHDDEQTLLRVDEAINKTYTRRNGAEMS"/> <has_n_lines n="18795" delta='3'/> </assert_contents> </output> <output name="samples" ftype="json"> <assert_contents> <has_n_lines n="22" delta='3'/> </assert_contents> </output> <output name="summary_statistics" ftype="txt"> <assert_contents> <has_text text="Soft core genes"/> <has_n_lines n="6" delta='3'/> </assert_contents> </output> </test> <!--Test 2: PanTA main test for gff files: Tests the 'dont_split' parameter --> <test expect_num_outputs="14"> <conditional name="mode"> <param name="select_mode" value="main"/> </conditional> <conditional name="input_type"> <param name="input_type_selector" value="gff"/> <param name="input_gff"> <collection type="list"> <element name="GCA_021342655.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021342655.1.gff"/> <element name="GCA_021534865.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021534865.1.gff"/> <element name="GCA_021697815.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021697815.1.gff"/> <element name="GCA_021890555.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021890555.1.gff"/> </collection> </param> </conditional> <param name="table" value="10"/> <param name="dont_split" value="true"/> <output name="annotated_clusters" ftype="json"> <assert_contents> <has_text text="GCA_021342655.1-NZ_JAJTPH010000093.1-5475-cds-WP_000557454.1"/> <has_n_lines n="90588" delta='3'/> </assert_contents> </output> <output name="blast_output" ftype="tsv"> <assert_contents> <has_text text="GCA_021342655.1-NZ_JAJTPH010000101.1-3-cds-WP_233337042.1"/> <has_n_lines n="30680" delta='3'/> </assert_contents> </output> <output name="clusters" ftype="json"> <assert_contents> <has_text text="GCA_021890555.1-NZ_JAKLOD010000002.1-4878-cds-L3T02_RS24235"/> <has_n_lines n="24266" delta='3'/> </assert_contents> </output> <output name="gene_annotation" ftype="csv"> <assert_contents> <has_text text="IclR family transcriptional regulator,6"/> <has_n_lines n="19712" delta='3'/> </assert_contents> </output> <output name="gene_position" ftype="csv"> <assert_contents> <has_text text="1-NZ_JAJTPH010000010.1-23-cds-LXO36_RS13380"/> <has_n_lines n="195" delta='3'/> </assert_contents> </output> <output name="gene_presence_absence" ftype="csv"> <assert_contents> <has_n_lines n="7089" delta='3'/> </assert_contents> </output> <output name="gene_presence_absence_Rtab" ftype="txt"> <assert_contents> <has_n_lines n="7089" delta='3'/> </assert_contents> </output> <output name="representative_clusters_nucl" ftype="fasta"> <assert_contents> <has_text text="GGTCTGCCCCACCGGCATCGACATTCGCGACGGCCTGCAGATCGAGTGCATTGGTTGCGC"/> <has_n_lines n="115793" delta='3'/> </assert_contents> </output> <output name="representative_clusters_prot" ftype="fasta"> <assert_contents> <has_text text="GLPHRHRHSRRPADRVHWLRRLHRCLRQHHGQDGLPQGPDQLHNRTQSFRTEDPSAAPTP"/> <has_n_lines n="45624" delta='3'/> </assert_contents> </output> <output name="representative" ftype="fasta"> <assert_contents> <has_text text="RIEGSVWPKSIRGSTPKVRGTCQIERAASESPHFMRFHVACPHCGEEQYLKFGDKETPFGLKWTPDDPSSVFYLCEHNACVIRQQELDFTDARYICEKTGIWTRDGILWFSSSGEEIEPPDSVTFHIWTAYSPFTTWVQIVKDWMKTKGDTGKRKTFVNTTLGETWEAKIGERPDAEVMAERKEHYSAPVPDRVAYLTAGIDSQLDRYEMRVWGWGPGEESWLIDRQIIMGRHDDEQTLLRVDEAINKTYTRRNGAEMS"/> <has_n_lines n="18795" delta='3'/> </assert_contents> </output> <output name="samples" ftype="json"> <assert_contents> <has_n_lines n="22" delta='3'/> </assert_contents> </output> <output name="summary_statistics" ftype="txt"> <assert_contents> <has_text text="Soft core genes"/> <has_n_lines n="6" delta='3'/> </assert_contents> </output> </test> <!--Test 3: PanTA main test for gff files: The 'alignment' parameter --> <test expect_num_outputs="14"> <conditional name="mode"> <param name="select_mode" value="main"/> </conditional> <conditional name="input_type"> <param name="input_type_selector" value="gff"/> <param name="input_gff"> <collection type="list"> <element name="GCA_021342655.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021342655.1.gff"/> <element name="GCA_021534865.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021534865.1.gff"/> <element name="GCA_021697815.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021697815.1.gff"/> <element name="GCA_021890555.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021890555.1.gff"/> </collection> </param> </conditional> <param name="table" value="10"/> <param name="alignment" value="nucleotide"/> <output name="annotated_clusters" ftype="json"> <assert_contents> <has_text text="GCA_021342655.1-NZ_JAJTPH010000093.1-5475-cds-WP_000557454.1"/> <has_n_lines n="96508" delta='3'/> </assert_contents> </output> <output name="blast_output" ftype="tsv"> <assert_contents> <has_text text="GCA_021342655.1-NZ_JAJTPH010000101.1-3-cds-WP_233337042.1"/> <has_n_lines n="30680" delta='3'/> </assert_contents> </output> <output name="clusters" ftype="json"> <assert_contents> <has_text text="GCA_021890555.1-NZ_JAKLOD010000002.1-4878-cds-L3T02_RS24235"/> <has_n_lines n="24266" delta='3'/> </assert_contents> </output> <output name="gene_annotation" ftype="csv"> <assert_contents> <has_text text="IclR family transcriptional regulator,6"/> <has_n_lines n="19712" delta='3'/> </assert_contents> </output> <output name="gene_position" ftype="csv"> <assert_contents> <has_text text="1-NZ_JAJTPH010000010.1-23-cds-LXO36_RS13380"/> <has_n_lines n="195" delta='3'/> </assert_contents> </output> <output name="gene_presence_absence" ftype="csv"> <assert_contents> <has_n_lines n="7681" delta='3'/> </assert_contents> </output> <output name="gene_presence_absence_Rtab" ftype="txt"> <assert_contents> <has_n_lines n="7681" delta='3'/> </assert_contents> </output> <output name="representative_clusters_nucl" ftype="fasta"> <assert_contents> <has_text text="GGTCTGCCCCACCGGCATCGACATTCGCGACGGCCTGCAGATCGAGTGCATTGGTTGCGC"/> <has_n_lines n="124180" delta='3'/> </assert_contents> </output> <output name="representative_clusters_prot" ftype="fasta"> <assert_contents> <has_text text="GLPHRHRHSRRPADRVHWLRRLHRCLRQHHGQDGLPQGPDQLHNRTQSFRTEDPSAAPTP"/> <has_n_lines n="49014" delta='3'/> </assert_contents> </output> <output name="representative" ftype="fasta"> <assert_contents> <has_text text="RIEGSVWPKSIRGSTPKVRGTCQIERAASESPHFMRFHVACPHCGEEQYLKFGDKETPFGLKWTPDDPSSVFYLCEHNACVIRQQELDFTDARYICEKTGIWTRDGILWFSSSGEEIEPPDSVTFHIWTAYSPFTTWVQIVKDWMKTKGDTGKRKTFVNTTLGETWEAKIGERPDAEVMAERKEHYSAPVPDRVAYLTAGIDSQLDRYEMRVWGWGPGEESWLIDRQIIMGRHDDEQTLLRVDEAINKTYTRRNGAEMS"/> <has_n_lines n="18795" delta='3'/> </assert_contents> </output> <output name="samples" ftype="json"> <assert_contents> <has_n_lines n="22" delta='3'/> </assert_contents> </output> <output name="summary_statistics" ftype="txt"> <assert_contents> <has_text text="Soft core genes"/> <has_n_lines n="6" delta='3'/> </assert_contents> </output> <output name="core_gene_alignment" ftype="fasta"> <assert_contents> <has_n_lines n="96130" delta='3'/> </assert_contents> </output> <output name="pan_genome_reference" ftype="fasta"> <assert_contents> <has_text text="AAAGGCGTTTGGTATATAACGATGCCAG"/> <has_n_lines n="84292" delta='3'/> </assert_contents> </output> </test> <!--Test 4: Basic PanTA add test for gff files: Tests the basic command for PanTA add --> <test expect_num_outputs="14"> <conditional name="mode"> <param name="select_mode" value="add"/> <param name="collection_dir" location="https://zenodo.org/records/16568442/files/collection_dir.tar.gz" ftype="tar.gz"/> </conditional> <conditional name="input_type"> <param name="input_type_selector" value="gff"/> <param name="input_gff"> <collection type="list"> <element name="GCA_021342735.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021342735.1.gff"/> <element name="GCA_021725855.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021725855.1.gff"/> <element name="GCA_021890695.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021890695.1.gff"/> </collection> </param> </conditional> <param name="table" value="10"/> <output name="annotated_clusters" ftype="json"> <assert_contents> <has_text text="GCA_021342655.1-NZ_JAJTPH010000093.1-5475-cds-WP_000557454.1"/> <has_n_lines n="118811" delta='3'/> </assert_contents> </output> <output name="blast_output" ftype="tsv"> <assert_contents> <has_text text="GCA_021342655.1-NZ_JAJTPH010000101.1-3-cds-WP_233337042.1"/> <has_n_lines n="38245" delta='3'/> </assert_contents> </output> <output name="clusters" ftype="json"> <assert_contents> <has_text text="GCA_021890555.1-NZ_JAKLOD010000002.1-4878-cds-L3T02_RS24235"/> <has_n_lines n="39790" delta='3'/> </assert_contents> </output> <output name="gene_annotation" ftype="csv"> <assert_contents> <has_text text="IclR family transcriptional regulator,6"/> <has_n_lines n="33564" delta='3'/> </assert_contents> </output> <output name="gene_position" ftype="csv"> <assert_contents> <has_text text="1-NZ_JAJTPH010000010.1-23-cds-LXO36_RS13380"/> <has_n_lines n="363" delta='3'/> </assert_contents> </output> <output name="gene_presence_absence" ftype="csv"> <assert_contents> <has_n_lines n="8523" delta='3'/> </assert_contents> </output> <output name="gene_presence_absence_Rtab" ftype="txt"> <assert_contents> <has_n_lines n="8523" delta='3'/> </assert_contents> </output> <output name="representative_clusters_nucl" ftype="fasta"> <assert_contents> <has_text text="GGTCTGCCCCACCGGCATCGACATTCGCGACGGCCTGCAGATCGAGTGCATTGGTTGCGC"/> <has_n_lines n="136572" delta='3'/> </assert_contents> </output> <output name="representative_clusters_prot" ftype="fasta"> <assert_contents> <has_text text="GLPHRHRHSRRPADRVHWLRRLHRCLRQHHGQDGLPQGPDQLHNRTQSFRTEDPSAAPTP"/> <has_n_lines n="53952" delta='3'/> </assert_contents> </output> <output name="representative" ftype="fasta"> <assert_contents> <has_text text="RIEGSVWPKSIRGSTPKVRGTCQIERAASESPHFMRFHVACPHCGEEQYLKFGDKETPFGLKWTPDDPSSVFYLCEHNACVIRQQELDFTDARYICEKTGIWTRDGILWFSSSGEEIEPPDSVTFHIWTAYSPFTTWVQIVKDWMKTKGDTGKRKTFVNTTLGETWEAKIGERPDAEVMAERKEHYSAPVPDRVAYLTAGIDSQLDRYEMRVWGWGPGEESWLIDRQIIMGRHDDEQTLLRVDEAINKTYTRRNGAEMS"/> <has_n_lines n="29001" delta='3'/> </assert_contents> </output> <output name="samples" ftype="json"> <assert_contents> <has_n_lines n="37" delta='3'/> </assert_contents> </output> <output name="summary_statistics" ftype="txt"> <assert_contents> <has_text text="Soft core genes"/> <has_n_lines n="6" delta='3'/> </assert_contents> </output> </test> <!--Test 5: Basic PanTA add test for gff files: Tests the 'dont_split' parameter --> <test expect_num_outputs="14"> <conditional name="mode"> <param name="select_mode" value="add"/> <param name="collection_dir" location="https://zenodo.org/records/16568442/files/collection_dir.tar.gz" ftype="tar.gz"/> </conditional> <conditional name="input_type"> <param name="input_type_selector" value="gff"/> <param name="input_gff"> <collection type="list"> <element name="GCA_021342735.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021342735.1.gff"/> <element name="GCA_021725855.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021725855.1.gff"/> <element name="GCA_021890695.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021890695.1.gff"/> </collection> </param> </conditional> <param name="table" value="10"/> <param name="dont_split" value="true"/> <output name="annotated_clusters" ftype="json"> <assert_contents> <has_text text="GCA_021342655.1-NZ_JAJTPH010000093.1-5475-cds-WP_000557454.1"/> <has_n_lines n="111811" delta='3'/> </assert_contents> </output> <output name="blast_output" ftype="tsv"> <assert_contents> <has_text text="GCA_021342655.1-NZ_JAJTPH010000101.1-3-cds-WP_233337042.1"/> <has_n_lines n="38245" delta='3'/> </assert_contents> </output> <output name="clusters" ftype="json"> <assert_contents> <has_text text="GCA_021890555.1-NZ_JAKLOD010000002.1-4878-cds-L3T02_RS24235"/> <has_n_lines n="39790" delta='3'/> </assert_contents> </output> <output name="gene_annotation" ftype="csv"> <assert_contents> <has_text text="IclR family transcriptional regulator,6"/> <has_n_lines n="33564" delta='3'/> </assert_contents> </output> <output name="gene_position" ftype="csv"> <assert_contents> <has_text text="1-NZ_JAJTPH010000010.1-23-cds-LXO36_RS13380"/> <has_n_lines n="363" delta='3'/> </assert_contents> </output> <output name="gene_presence_absence" ftype="csv"> <assert_contents> <has_n_lines n="7825" delta='3'/> </assert_contents> </output> <output name="gene_presence_absence_Rtab" ftype="txt"> <assert_contents> <has_n_lines n="7825" delta='3'/> </assert_contents> </output> <output name="representative_clusters_nucl" ftype="fasta"> <assert_contents> <has_text text="GGTCTGCCCCACCGGCATCGACATTCGCGACGGCCTGCAGATCGAGTGCATTGGTTGCGC"/> <has_n_lines n="126631" delta='3'/> </assert_contents> </output> <output name="representative_clusters_prot" ftype="fasta"> <assert_contents> <has_text text="GLPHRHRHSRRPADRVHWLRRLHRCLRQHHGQDGLPQGPDQLHNRTQSFRTEDPSAAPTP"/> <has_n_lines n="49946" delta='3'/> </assert_contents> </output> <output name="representative" ftype="fasta"> <assert_contents> <has_text text="RIEGSVWPKSIRGSTPKVRGTCQIERAASESPHFMRFHVACPHCGEEQYLKFGDKETPFGLKWTPDDPSSVFYLCEHNACVIRQQELDFTDARYICEKTGIWTRDGILWFSSSGEEIEPPDSVTFHIWTAYSPFTTWVQIVKDWMKTKGDTGKRKTFVNTTLGETWEAKIGERPDAEVMAERKEHYSAPVPDRVAYLTAGIDSQLDRYEMRVWGWGPGEESWLIDRQIIMGRHDDEQTLLRVDEAINKTYTRRNGAEMS"/> <has_n_lines n="29001" delta='3'/> </assert_contents> </output> <output name="samples" ftype="json"> <assert_contents> <has_n_lines n="37" delta='3'/> </assert_contents> </output> <output name="summary_statistics" ftype="txt"> <assert_contents> <has_text text="Soft core genes"/> <has_n_lines n="6" delta='3'/> </assert_contents> </output> </test> <!--Test 6: Basic PanTA add test for gff files: Tests the 'alignment' parameter --> <test expect_num_outputs="14"> <conditional name="mode"> <param name="select_mode" value="add"/> <param name="collection_dir" location="https://zenodo.org/records/16568442/files/collection_dir.tar.gz" ftype="tar.gz"/> </conditional> <conditional name="input_type"> <param name="input_type_selector" value="gff"/> <param name="input_gff"> <collection type="list"> <element name="GCA_021342735.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021342735.1.gff"/> <element name="GCA_021725855.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021725855.1.gff"/> <element name="GCA_021890695.1.gff" location="https://zenodo.org/records/16568442/files/GCA_021890695.1.gff"/> </collection> </param> </conditional> <param name="table" value="10"/> <param name="alignment" value="nucleotide"/> <output name="annotated_clusters" ftype="json"> <assert_contents> <has_text text="GCA_021342655.1-NZ_JAJTPH010000093.1-5475-cds-WP_000557454.1"/> <has_n_lines n="118811" delta='3'/> </assert_contents> </output> <output name="blast_output" ftype="tsv"> <assert_contents> <has_text text="GCA_021342655.1-NZ_JAJTPH010000101.1-3-cds-WP_233337042.1"/> <has_n_lines n="38245" delta='3'/> </assert_contents> </output> <output name="clusters" ftype="json"> <assert_contents> <has_text text="GCA_021890555.1-NZ_JAKLOD010000002.1-4878-cds-L3T02_RS24235"/> <has_n_lines n="39790" delta='3'/> </assert_contents> </output> <output name="gene_annotation" ftype="csv"> <assert_contents> <has_text text="IclR family transcriptional regulator,6"/> <has_n_lines n="33564" delta='3'/> </assert_contents> </output> <output name="gene_position" ftype="csv"> <assert_contents> <has_text text="1-NZ_JAJTPH010000010.1-23-cds-LXO36_RS13380"/> <has_n_lines n="363" delta='3'/> </assert_contents> </output> <output name="gene_presence_absence" ftype="csv"> <assert_contents> <has_n_lines n="8523" delta='3'/> </assert_contents> </output> <output name="gene_presence_absence_Rtab" ftype="txt"> <assert_contents> <has_n_lines n="8523" delta='3'/> </assert_contents> </output> <output name="representative_clusters_nucl" ftype="fasta"> <assert_contents> <has_text text="GGTCTGCCCCACCGGCATCGACATTCGCGACGGCCTGCAGATCGAGTGCATTGGTTGCGC"/> <has_n_lines n="136572" delta='3'/> </assert_contents> </output> <output name="representative_clusters_prot" ftype="fasta"> <assert_contents> <has_text text="GLPHRHRHSRRPADRVHWLRRLHRCLRQHHGQDGLPQGPDQLHNRTQSFRTEDPSAAPTP"/> <has_n_lines n="53952" delta='3'/> </assert_contents> </output> <output name="representative" ftype="fasta"> <assert_contents> <has_text text="RIEGSVWPKSIRGSTPKVRGTCQIERAASESPHFMRFHVACPHCGEEQYLKFGDKETPFGLKWTPDDPSSVFYLCEHNACVIRQQELDFTDARYICEKTGIWTRDGILWFSSSGEEIEPPDSVTFHIWTAYSPFTTWVQIVKDWMKTKGDTGKRKTFVNTTLGETWEAKIGERPDAEVMAERKEHYSAPVPDRVAYLTAGIDSQLDRYEMRVWGWGPGEESWLIDRQIIMGRHDDEQTLLRVDEAINKTYTRRNGAEMS"/> <has_n_lines n="29001" delta='3'/> </assert_contents> </output> <output name="samples" ftype="json"> <assert_contents> <has_n_lines n="37" delta='3'/> </assert_contents> </output> <output name="summary_statistics" ftype="txt"> <assert_contents> <has_text text="Soft core genes"/> <has_n_lines n="6" delta='3'/> </assert_contents> </output> </test> </tests> <help><![CDATA[ PanTA builds the pangenome of a large collection of genomes and adds a set of new genomes to an existing pangenome without rebuilding the accumulated pangenome from scratch. PanTA takes as input a list of genome assemblies and their annotations. It extracts the protein-coding regions as specified by the annotations and translates them into protein sequences. PanTA then generates output reports according to the standards set out by Roary, which include a spreadsheet detailing the presence and absence of each gene in each isolate as well as a summary of pangenome statistics. **INPUTS** - A collection of gff3 files or a tsv file. **OUTPUTS** - annotated_clusters.json - blast.tsv - clusters.json - gene_annotation.csv - gene_position.csv - gene_presence_absence.csv - gene_presence_absence.Rtab - representative_clusters_nucl.fasta - representative_clusters_prot.fasta - representative.fasta - samples.json - summary_statistics.txt - core_gene_alignment.aln.gz (requires alignment option) - pan_genome_reference.fna (requires alignment option) ]]></help> <citations> <citation type="doi">10.6084/m9.figshare.23724705</citation> </citations> <expand macro="creator"/> </tool>