Mercurial > repos > bgruening > mitohifi
changeset 2:bfab6f5b449d draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit 3faa0723d5faf734d8821626bbd31a614b25aafb
author | bgruening |
---|---|
date | Tue, 06 May 2025 13:36:26 +0000 |
parents | 99ddbf037d98 |
children | |
files | macros.xml mitohifi.xml |
diffstat | 2 files changed, 167 insertions(+), 152 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Wed May 03 19:33:09 2023 +0000 +++ b/macros.xml Tue May 06 13:36:26 2025 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">3</token> - <token name="@GALAXY_TOOL_VERSION@">galaxy0</token> + <token name="@TOOL_VERSION@">3.2.3</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0196</edam_topic> @@ -11,7 +11,7 @@ </xml> <xml name="requirements"> <requirements> - <container type="docker">quay.io/bgruening/mitohifi:3_galaxy0</container> + <container type="docker">ghcr.io/marcelauliano/mitohifi:@TOOL_VERSION@</container> </requirements> </xml> <xml name="citations">
--- a/mitohifi.xml Wed May 03 19:33:09 2023 +0000 +++ b/mitohifi.xml Tue May 06 13:36:26 2025 +0000 @@ -1,10 +1,10 @@ -<tool id='mitohifi' name='MitoHiFi' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'> - <description>assembly mitogenomes from Pacbio HiFi reads</description> +<tool id='mitohifi' name='MitoHiFi' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@' profile='23.2'> + <description>Assemble mitogenomes from Pacbio HiFi reads</description> <macros> <import>macros.xml</import> </macros> - <expand macro='edam_ontology' /> - <expand macro='requirements' /> + <expand macro='edam_ontology'/> + <expand macro='requirements'/> <command detect_errors='exit_code'><![CDATA[ #if $operation_mode.command == 'find_reference' findMitoReference.py @@ -30,6 +30,7 @@ #end if -f related_mito.fasta -g related_mito.gb + -a $operation_mode.organism_selection #if $operation_mode.advanced_options.query_blast -p $operation_mode.advanced_options.query_blast #end if @@ -71,7 +72,7 @@ </sanitizer> </param> <param argument="--min_length" type="integer" - min="0" max="15000000" value="" optional="True" label="Minimal appropriate length" /> + min="0" max="15000000" value="" optional="True" label="Minimal appropriate length"/> <param name="exact_species" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="False" optional="True" label="Search for an exact species"/> </when> @@ -94,11 +95,16 @@ </when> </conditional> <param name="reference_fasta" argument="-f" type="data" - format="fasta,fasta.gz" multiple="True" label="Close-related mitogenome in fasta format" + format="fasta,fasta.gz" label="Close-related mitogenome in fasta format" help="Close-related mitogenome is fasta format"/> <param name="reference_genbank" argument="-g" type="data" - format="genbank,genbank.gz" multiple="True" optional="True" label="Close-related mitogenome in genbank format" + format="genbank,genbank.gz" label="Close-related mitogenome in genbank format" help="Close-related mitogenome is genbank format"/> + <param name="organism_selection" argument="-a" type="select" label="Choose between animal or plant"> + <option value="animal" selected="true">Animal</option> + <option value="plant">Plant</option> + <option value="fungal">Fungal</option> + </param> <param name="genetic_code" type="select" label="Genetic code" help="Organism genetic code following NCBI table (for mitogenome annotation)"> <option value="1">Standard code</option> <option value="2">Vertebrate mitochondrial code</option> @@ -122,13 +128,13 @@ <section name="advanced_options" title="Advanced options"> <param name="query_blast" argument="-p" type="integer" min="0" max="100" value="" optional="True" label="Blast percentage identity" - help="Percentage of query in the blast match with close-related mito. By default it is going to chose any contig which has 50% or more of its length in the blast match." /> + help="Percentage of query in the blast match with close-related mito. By default it is going to chose any contig which has 50% or more of its length in the blast match."/> <param argument="--circular-size" type="integer" min="0" max="15000000" value="" optional="True" label="Estimated mtDNA size" - help="Size to consider when checking for circularization" /> + help="Size to consider when checking for circularization"/> <param argument="--circular_offset" type="integer" min="0" max="5000" value="" optional="True" label="Circularization offset" - help="Offset from start and finish to consider when looking for circularization" /> + help="Offset from start and finish to consider when looking for circularization"/> <param name="outputs" type="select" label="Optional outputs" multiple="True" display="checkboxes"> <option value="contigs_filtering">Contigs filtering</option> <option value="contigs_circularization">Contigs circularization</option> @@ -136,7 +142,7 @@ <option value="final_mitogenome_alignment">Final mitogenome alignment</option> </param> </section> - <param name="output_zip" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate an output package in ZIP format" help="This option creates a zip file with all the files and folders generated by MitoHiFi." /> + <param name="output_zip" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate an output package in ZIP format" help="This option creates a zip file with all the files and folders generated by MitoHiFi."/> </when> </conditional> </inputs> @@ -175,7 +181,7 @@ <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_circularization' in operation_mode['advanced_options']['outputs'])</filter> </data> <collection name="potential_contigs" type='list' label='${tool.name} on ${on_string}: potential contigs'> - <discover_datasets pattern='__designation_and_ext__' format='txt' directory='potential_contigs' /> + <discover_datasets pattern='__designation_and_ext__' format='txt' directory='potential_contigs'/> <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'potential_contigs' in operation_mode['advanced_options']['outputs'])</filter> </collection> <data name="final_mitogenome" format="fasta" from_work_dir="final_mitogenome_choice/all_mitogenomes.rotated.aligned.fa" label="${tool.name} on ${on_string}: mitogenomes alignment"> @@ -205,19 +211,19 @@ </conditional> <output name="fasta_reference" ftype="fasta"> <assert_contents> - <has_size value="15593"/> - <has_line line=">NC_062101.1 Condica capensis mitochondrion, complete genome"/> + <has_size value="15662" delta="200"/> + <has_line line=">OQ539671.1 Amphipyra erebina mitochondrion, complete genome"/> </assert_contents> </output> <output name="genbank_reference" ftype="genbank"> <assert_contents> - <has_size value="43220"/> - <has_line line="DEFINITION Condica capensis mitochondrion, complete genome."/> + <has_size value="35605" delta="200"/> + <has_line line="DEFINITION Amphipyra erebina mitochondrion, complete genome."/> </assert_contents> </output> </test> <!--Test 02--> - <!--<test expect_num_outputs="8"> + <test expect_num_outputs="8"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> <conditional name="input_option"> @@ -230,36 +236,36 @@ </conditional> <output name="mitogenome_fasta" ftype="fasta"> <assert_contents> - <has_size value="15337"/> - <has_line line=">ptg000001c_rotated"/> + <has_size value="15603" delta="200"/> + <has_line line=">ptg000001l_rotated ptg000001l"/> </assert_contents> </output> <output name="mitogenome_genbank" ftype="genbank"> <assert_contents> - <has_size value="30637"/> - <has_line line="DEFINITION ptg000001c_rotated"/> + <has_size value="30548" delta="200"/> + <has_line line="DEFINITION ptg000001l."/> </assert_contents> </output> <output name="hifiasm" ftype="fasta"> <assert_contents> - <has_size value="2063025"/> + <has_size value="1956147"/> <has_line line=">m64094_200908_163909/67999/ccs"/> </assert_contents> </output> <output name="hifiasm_filtered" ftype="fasta"> <assert_contents> - <has_size value="2097153"/> + <has_size value="1988506"/> <has_line line=">m64094_200908_163909/1605/ccs"/> </assert_contents> </output> <output name="hifiasm_contigs" ftype="fasta"> <assert_contents> - <has_size value="15329"/> - <has_line line=">ptg000001c"/> + <has_size value="30246"/> + <has_line line=">ptg000001l"/> </assert_contents> </output> - </test>--> - <!--Test 03--> + </test> + <!--Test 03--> <test expect_num_outputs="8"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> @@ -276,36 +282,36 @@ </conditional> <output name="mitogenome_fasta" ftype="fasta"> <assert_contents> - <has_size value="15337"/> - <has_line line=">ptg000001c_rotated"/> + <has_size value="15603"/> + <has_line line=">ptg000001l_rotated ptg000001l"/> </assert_contents> </output> <output name="mitogenome_genbank" ftype="genbank"> <assert_contents> - <has_size value="30637"/> - <has_line line="DEFINITION ptg000001c_rotated"/> + <has_size value="30548"/> + <has_line line="DEFINITION ptg000001l."/> </assert_contents> </output> <output name="hifiasm" ftype="fasta"> <assert_contents> - <has_size value="4123737"/> + <has_size value="3963527"/> <has_line line=">m64094_200908_163909/67999/ccs"/> </assert_contents> </output> <output name="hifiasm_filtered" ftype="fasta"> <assert_contents> - <has_size value="4191948"/> + <has_size value="4029085"/> <has_line line=">m64094_200908_163909/1605/ccs"/> </assert_contents> </output> <output name="hifiasm_contigs" ftype="fasta"> <assert_contents> - <has_size value="15329"/> - <has_line line=">ptg000001c"/> + <has_size value="30246"/> + <has_line line=">ptg000001l"/> </assert_contents> </output> </test> - <!--Test 04--> + <!--Test 04--> <test expect_num_outputs="8"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> @@ -322,36 +328,83 @@ </conditional> <output name="mitogenome_fasta" ftype="fasta"> <assert_contents> - <has_size value="15337"/> - <has_line line=">ptg000001c_rotated"/> + <has_size value="15603"/> + <has_line line=">ptg000001l_rotated ptg000001l"/> </assert_contents> </output> <output name="mitogenome_genbank" ftype="genbank"> <assert_contents> - <has_size value="30637"/> - <has_line line="DEFINITION ptg000001c_rotated"/> + <has_size value="30548"/> + <has_line line="DEFINITION ptg000001l."/> </assert_contents> </output> <output name="hifiasm" ftype="fasta"> <assert_contents> - <has_size value="4123737"/> + <has_size value="3963527"/> <has_line line=">m64094_200908_163909/67999/ccs"/> </assert_contents> </output> <output name="hifiasm_filtered" ftype="fasta"> <assert_contents> - <has_size value="4191948"/> + <has_size value="4029085"/> <has_line line=">m64094_200908_163909/1605/ccs"/> </assert_contents> </output> <output name="hifiasm_contigs" ftype="fasta"> <assert_contents> - <has_size value="15329"/> - <has_line line=">ptg000001c"/> + <has_size value="30246"/> + <has_line line=">ptg000001l"/> + </assert_contents> + </output> + </test> + <!--Test 05 --> + <test expect_num_outputs="8"> + <conditional name="operation_mode"> + <param name="command" value="mitohifi"/> + <conditional name="input_option"> + <param name="input" value="pacbio"/> + <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> + </conditional> + <param name="reference_fasta" value="related_mitogenome.fasta"/> + <param name="reference_genbank" value="related_mitogenome.gb"/> + <param name="organism_selection" value="plant"/> + <param name="genetic_code" value="5"/> + <section name="advanced_options"> + <param name="circular_size" value="120000"/> + </section> + </conditional> + <output name="mitogenome_fasta" ftype="fasta"> + <assert_contents> + <has_size value="15603"/> + <has_line line=">ptg000001l_rotated ptg000001l"/> </assert_contents> </output> - </test> - <!--Test 05--> + <output name="mitogenome_genbank" ftype="genbank"> + <assert_contents> + <has_size value="30548"/> + <has_line line="DEFINITION ptg000001l."/> + </assert_contents> + </output> + <output name="hifiasm" ftype="fasta"> + <assert_contents> + <has_size value="3963527"/> + <has_line line=">m64094_200908_163909/67999/ccs"/> + </assert_contents> + </output> + <output name="hifiasm_filtered" ftype="fasta"> + <assert_contents> + <has_size value="4029085"/> + <has_line line=">m64094_200908_163909/1605/ccs"/> + </assert_contents> + </output> + <output name="hifiasm_contigs" ftype="fasta"> + <assert_contents> + <has_size value="30246"/> + <has_line line=">ptg000001l"/> + </assert_contents> + </output> + </test> + <!--Test 06 --> <test expect_num_outputs="8"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> @@ -368,36 +421,36 @@ </conditional> <output name="mitogenome_fasta" ftype="fasta"> <assert_contents> - <has_size value="15337"/> - <has_line line=">ptg000001c_rotated"/> + <has_size value="15603"/> + <has_line line=">ptg000001l_rotated ptg000001l"/> </assert_contents> </output> <output name="mitogenome_genbank" ftype="genbank"> <assert_contents> - <has_size value="30637"/> - <has_line line="DEFINITION ptg000001c_rotated"/> + <has_size value="30548"/> + <has_line line="DEFINITION ptg000001l."/> </assert_contents> </output> <output name="hifiasm" ftype="fasta"> <assert_contents> - <has_size value="4123737"/> + <has_size value="3963527"/> <has_line line=">m64094_200908_163909/67999/ccs"/> </assert_contents> </output> <output name="hifiasm_filtered" ftype="fasta"> <assert_contents> - <has_size value="4191948"/> + <has_size value="4029085"/> <has_line line=">m64094_200908_163909/1605/ccs"/> </assert_contents> </output> <output name="hifiasm_contigs" ftype="fasta"> <assert_contents> - <has_size value="15329"/> - <has_line line=">ptg000001c"/> + <has_size value="30246"/> + <has_line line=">ptg000001l"/> </assert_contents> </output> - </test> - <!--Test 06--> + </test> + <!--Test 07 --> <test expect_num_outputs="11"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> @@ -414,52 +467,51 @@ </conditional> <output name="mitogenome_fasta" ftype="fasta"> <assert_contents> - <has_size value="15337"/> - <has_line line=">ptg000001c_rotated"/> + <has_size value="15603"/> + <has_line line=">ptg000001l_rotated ptg000001l"/> </assert_contents> </output> <output name="mitogenome_genbank" ftype="genbank"> <assert_contents> - <has_size value="30637"/> - <has_line line="DEFINITION ptg000001c_rotated"/> + <has_size value="30548"/> + <has_line line="DEFINITION ptg000001l."/> </assert_contents> </output> <output name="hifiasm" ftype="fasta"> <assert_contents> - <has_size value="4123737"/> + <has_size value="3963527"/> <has_line line=">m64094_200908_163909/67999/ccs"/> </assert_contents> </output> <output name="hifiasm_filtered" ftype="fasta"> <assert_contents> - <has_size value="4191948"/> - <!--<has_line line=">m64094_200908_163909/1605/ccs"/>--> + <has_size value="4029085"/> </assert_contents> </output> <output name="hifiasm_contigs" ftype="fasta"> <assert_contents> - <has_size value="15329"/> - <has_line line=">ptg000001c"/> + <has_size value="30246"/> + <has_line line=">ptg000001l"/> </assert_contents> </output> <output name="parsed_blast" ftype="txt"> <assert_contents> - <has_size value="104"/> + <has_size value="105"/> </assert_contents> </output> <output name="parsed_blast_all" ftype="txt"> <assert_contents> - <has_size value="104"/> + <has_size value="105"/> </assert_contents> </output> <output name="contigs_ids" ftype="txt"> <assert_contents> <has_size value="11"/> - <has_line line="ptg000001c"/> + <has_line line="ptg000001l"/> </assert_contents> </output> </test> - <!--Test 07--> + <!--Test 08 --> <test expect_num_outputs="9"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> @@ -476,94 +528,42 @@ </conditional> <output name="mitogenome_fasta" ftype="fasta"> <assert_contents> - <has_size value="15337"/> - <has_line line=">ptg000001c_rotated"/> + <has_size value="15603"/> + <has_line line=">ptg000001l_rotated ptg000001l"/> </assert_contents> </output> <output name="mitogenome_genbank" ftype="genbank"> <assert_contents> - <has_size value="30637"/> - <has_line line="DEFINITION ptg000001c_rotated"/> + <has_size value="30548"/> + <has_line line="DEFINITION ptg000001l."/> </assert_contents> </output> <output name="hifiasm" ftype="fasta"> <assert_contents> - <has_size value="4123737"/> + <has_size value="3963527"/> <has_line line=">m64094_200908_163909/67999/ccs"/> </assert_contents> </output> <output name="hifiasm_filtered" ftype="fasta"> <assert_contents> - <has_size value="4191948"/> + <has_size value="4029085"/> <has_line line=">m64094_200908_163909/1605/ccs"/> </assert_contents> </output> <output name="hifiasm_contigs" ftype="fasta"> <assert_contents> - <has_size value="15329"/> - <has_line line=">ptg000001c"/> - </assert_contents> - </output> - <output name="contigs_circularization" ftype="txt"> - <assert_contents> - <has_size value="28"/> - </assert_contents> - </output> - </test> - <!--Test 08--> - <test expect_num_outputs="9"> - <conditional name="operation_mode"> - <param name="command" value="mitohifi"/> - <conditional name="input_option"> - <param name='input' value="pacbio"/> - <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/> - </conditional> - <param name="reference_fasta" value="related_mitogenome.fasta"/> - <param name="reference_genbank" value="related_mitogenome.gb"/> - <param name="genetic_code" value="5"/> - <section name="advanced_options"> - <param name="outputs" value="contigs_circularization"/> - </section> - </conditional> - <output name="mitogenome_fasta" ftype="fasta"> - <assert_contents> - <has_size value="15337"/> - <has_line line=">ptg000001c_rotated"/> + <has_size value="30246"/> + <has_line line=">ptg000001l"/> </assert_contents> </output> - <output name="mitogenome_genbank" ftype="genbank"> + <output name="contigs_circularization"> <assert_contents> - <has_size value="30637"/> - <has_line line="DEFINITION ptg000001c_rotated"/> - </assert_contents> - </output> - <output name="hifiasm" ftype="fasta"> - <assert_contents> - <has_size value="4123737"/> - <has_line line=">m64094_200908_163909/67999/ccs"/> + <has_size value="55"/> </assert_contents> </output> - <output name="hifiasm_filtered" ftype="fasta"> - <assert_contents> - <has_size value="4191948"/> - <has_line line=">m64094_200908_163909/1605/ccs"/> - </assert_contents> - </output> - <output name="hifiasm_contigs" ftype="fasta"> - <assert_contents> - <has_size value="15329"/> - <has_line line=">ptg000001c"/> - </assert_contents> - </output> - <output name="final_mitogenome" ftype="fasta"> - <assert_contents> - <has_size value="15329"/> - <has_line line=">ptg000001c"/> - </assert_contents> - </output> - </test> - <!--Test 09--> - <test expect_num_outputs="2"> + </test> + <!--Test 09 --> + <test expect_num_outputs="5"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> <conditional name="input_option"> @@ -576,18 +576,33 @@ </conditional> <output name="mitogenome_fasta" ftype="fasta"> <assert_contents> - <has_size value="15684"/> + <has_size value="15944"/> <has_line line=">NC_016067.1_rc_rotated"/> </assert_contents> </output> <output name="mitogenome_genbank" ftype="genbank"> <assert_contents> - <has_size value="31407"/> - <has_line line="DEFINITION NC_016067.1_rc_rotated"/> + <has_size value="31411"/> + <has_line line="ACCESSION NC_016067.1_rc_rotated"/> + </assert_contents> + </output> + <output name="mitogenome_genbank" ftype="genbank"> + <assert_contents> + <has_line line="ACCESSION NC_016067.1_rc_rotated"/> + </assert_contents> + </output> + <output name="mitogenome_annotation" ftype="png"> + <assert_contents> + <has_size value="67255"/> + </assert_contents> + </output> + <output name="contigs_stats" ftype="tsv"> + <assert_contents> + <has_n_lines n="4"/> </assert_contents> </output> </test> - <!--Test 10--> + <!--Test 10 --> <test expect_num_outputs="9"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> @@ -602,40 +617,40 @@ </conditional> <output name="mitogenome_fasta" ftype="fasta"> <assert_contents> - <has_size value="15337"/> - <has_line line=">ptg000001c_rotated"/> + <has_size value="15603"/> + <has_line line=">ptg000001l_rotated ptg000001l"/> </assert_contents> </output> <output name="mitogenome_genbank" ftype="genbank"> <assert_contents> - <has_size value="30637"/> - <has_line line="DEFINITION ptg000001c_rotated"/> + <has_size value="30548"/> + <has_line line="DEFINITION ptg000001l."/> </assert_contents> </output> <output name="hifiasm" ftype="fasta"> <assert_contents> - <has_size value="4123737"/> + <has_size value="3963527"/> <has_line line=">m64094_200908_163909/67999/ccs"/> </assert_contents> </output> <output name="hifiasm_filtered" ftype="fasta"> <assert_contents> - <has_size value="4191948"/> + <has_size value="4029085"/> <has_line line=">m64094_200908_163909/1605/ccs"/> </assert_contents> </output> <output name="hifiasm_contigs" ftype="fasta"> <assert_contents> - <has_size value="15329"/> - <has_line line=">ptg000001c"/> + <has_size value="30246"/> + <has_line line=">ptg000001l"/> </assert_contents> </output> <output name="zip_file" ftype="zip"> <assert_contents> - <has_size value="5418006" delta="100"/> + <has_size value="5190456" delta="100"/> </assert_contents> </output> - </test> + </test> </tests> <help><![CDATA[ .. class:: infomark @@ -653,5 +668,5 @@ ]]> </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>