Mercurial > repos > iuc > panta
diff panta.xml @ 0:72296762b4f1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta/ commit 9b05e32c37a0825eb503df9daaf39b9c48e07c5b
| author | iuc |
|---|---|
| date | Mon, 15 Sep 2025 11:40:14 +0000 |
| parents | |
| children | b50893534705 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/panta.xml Mon Sep 15 11:40:14 2025 +0000 @@ -0,0 +1,712 @@ +<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 $input_type.input_gff + #set identifier = re.sub('[^\s\w\-\\.]','_',str($gff.element_identifier)) + ln -fs '$gff' '$input_directory/$identifier' && + #end for + #elif $input_type.input_type_selector == "tsv": + #set identifier = re.sub('[^\s\w\-\\.]','_',str($input_type.input_tsv.element_identifier)) + ln -fs '$input_type.input_tsv' '$input_directory/$identifier' && + #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" 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 ${on_string} : Summary Statistics" from_work_dir="out/summary_statistics.txt"/> + + <!--Alignment outputs --> + <data format="txt" name="core_gene_alignment" label="${tool.name} on ${on_string} : Core Gene Alignment" from_work_dir="out/core_gene_alignment.aln.gz"> + <filter> ['alignment'] != 'None' </filter> + </data> + <data format="txt" name="pan_genome_reference" label="${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="txt"> + <assert_contents> + <has_n_lines n="96690" delta='3'/> + </assert_contents> + </output> + <output name="pan_genome_reference" ftype="txt"> + <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> \ No newline at end of file