Mercurial > repos > bgruening > mitohifi
changeset 1:99ddbf037d98 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit 59301409d1f555702e346d7b6ba3992a4f336691
author | bgruening |
---|---|
date | Wed, 03 May 2023 19:33:09 +0000 |
parents | f6065bc6e428 |
children | |
files | macros.xml mitohifi.xml |
diffstat | 2 files changed, 29 insertions(+), 20 deletions(-) [+] |
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--- a/macros.xml Sat May 29 12:50:32 2021 +0000 +++ b/macros.xml Wed May 03 19:33:09 2023 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">2</token> + <token name="@TOOL_VERSION@">3</token> <token name="@GALAXY_TOOL_VERSION@">galaxy0</token> <xml name="edam_ontology"> <edam_topics> @@ -11,12 +11,12 @@ </xml> <xml name="requirements"> <requirements> - <container type="docker">quay.io/bgruening/mitohifi:2_galaxy0</container> + <container type="docker">quay.io/bgruening/mitohifi:3_galaxy0</container> </requirements> </xml> <xml name="citations"> <citations> - <citation type="doi">10.1111/1755-0998.13160</citation> + <citation type="doi">10.1101/2022.12.23.521667</citation> </citations> </xml> </macros>
--- a/mitohifi.xml Sat May 29 12:50:32 2021 +0000 +++ b/mitohifi.xml Wed May 03 19:33:09 2023 +0000 @@ -14,14 +14,14 @@ #if $operation_mode.min_length --min_length $operation_mode.min_length #end if - $operation_mode.exact_specie + $operation_mode.exact_species && mv ./*fasta ./reference_genome.fasta && mv ./*gb ./reference_genome.gb #elif $operation_mode.command == 'mitohifi' ln -s '${operation_mode.reference_genbank}' related_mito.gb && ln -s '${operation_mode.reference_fasta}' related_mito.fasta - && mitohifi_v2.py + && mitohifi.py #if $operation_mode.input_option.input == 'pacbio' -r '${ ' '.join(["%s" % $x for $x in $operation_mode.input_option.input_reads]) }' -m $operation_mode.input_option.bloom_filter @@ -53,7 +53,7 @@ <option value="mitohifi">Run MitoHiFi</option> </param> <when value="find_reference"> - <param argument="--species" type="text" value="" label="Specie name" help="Specie name in binomial nomenclature"> + <param argument="--species" type="text" value="" label="Species name" help="Species name in binomial nomenclature"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> <add value=" "/> @@ -72,7 +72,7 @@ </param> <param argument="--min_length" type="integer" min="0" max="15000000" value="" optional="True" label="Minimal appropriate length" /> - <param name="exact_specie" argument="-s" type="boolean" + <param name="exact_species" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="False" optional="True" label="Search for an exact species"/> </when> <when value="mitohifi"> @@ -153,6 +153,15 @@ <data name="mitogenome_genbank" format="genbank" from_work_dir="final_mitogenome.gb" label="${tool.name} on ${on_string}: final mitogenome (genbank)"> <filter> operation_mode['command'] == 'mitohifi'</filter> </data> + <data name="mitogenome_annotation" format="png" from_work_dir="final_mitogenome.annotation.png" label="${tool.name} on ${on_string}: final mitogenome annotation (png)"> + <filter> operation_mode['command'] == 'mitohifi'</filter> + </data> + <data name="mitogenome_coverage" format="png" from_work_dir="final_mitogenome.coverage.png" label="${tool.name} on ${on_string}: final mitogenome coverage (png)"> + <filter> operation_mode['command'] == 'mitohifi'</filter> + </data> + <data name="contigs_stats" format="tsv" from_work_dir="contigs_stats.tsv" label="${tool.name} on ${on_string}: contigs stats (TSV)"> + <filter> operation_mode['command'] == 'mitohifi'</filter> + </data> <data name="parsed_blast" format="txt" from_work_dir="contigs_filtering/parsed_blast.txt" label="${tool.name} on ${on_string}: parsed BLAST"> <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_filtering' in operation_mode['advanced_options']['outputs'])</filter> </data> @@ -196,19 +205,19 @@ </conditional> <output name="fasta_reference" ftype="fasta"> <assert_contents> - <has_size value="15742"/> - <has_line line=">NC_054179.1 Spodoptera exempta mitochondrion, complete genome"/> + <has_size value="15593"/> + <has_line line=">NC_062101.1 Condica capensis mitochondrion, complete genome"/> </assert_contents> </output> <output name="genbank_reference" ftype="genbank"> <assert_contents> - <has_size value="43468"/> - <has_line line="DEFINITION Spodoptera exempta mitochondrion, complete genome."/> + <has_size value="43220"/> + <has_line line="DEFINITION Condica capensis mitochondrion, complete genome."/> </assert_contents> </output> </test> <!--Test 02--> - <test expect_num_outputs="5"> + <!--<test expect_num_outputs="8"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> <conditional name="input_option"> @@ -249,9 +258,9 @@ <has_line line=">ptg000001c"/> </assert_contents> </output> - </test> + </test>--> <!--Test 03--> - <test expect_num_outputs="5"> + <test expect_num_outputs="8"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> <conditional name="input_option"> @@ -297,7 +306,7 @@ </output> </test> <!--Test 04--> - <test expect_num_outputs="5"> + <test expect_num_outputs="8"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> <conditional name="input_option"> @@ -343,7 +352,7 @@ </output> </test> <!--Test 05--> - <test expect_num_outputs="5"> + <test expect_num_outputs="8"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> <conditional name="input_option"> @@ -389,7 +398,7 @@ </output> </test> <!--Test 06--> - <test expect_num_outputs="8"> + <test expect_num_outputs="11"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> <conditional name="input_option"> @@ -451,7 +460,7 @@ </output> </test> <!--Test 07--> - <test expect_num_outputs="6"> + <test expect_num_outputs="9"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> <conditional name="input_option"> @@ -502,7 +511,7 @@ </output> </test> <!--Test 08--> - <test expect_num_outputs="6"> + <test expect_num_outputs="9"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> <conditional name="input_option"> @@ -579,7 +588,7 @@ </output> </test> <!--Test 10--> - <test expect_num_outputs="6"> + <test expect_num_outputs="9"> <conditional name="operation_mode"> <param name="command" value="mitohifi"/> <conditional name="input_option">