Mercurial > repos > iuc > ncbi_datasets
diff macros.xml @ 10:a3395b1d871b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
author | iuc |
---|---|
date | Mon, 21 Nov 2022 11:40:05 +0000 |
parents | 18eed8fa7f23 |
children | ac24fff14f23 |
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--- a/macros.xml Wed Aug 24 13:00:58 2022 +0000 +++ b/macros.xml Mon Nov 21 11:40:05 2022 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">13.35.0</token> + <token name="@TOOL_VERSION@">14.3</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.01</token> <token name="@LICENSE@">MIT</token> @@ -11,28 +11,25 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement> - <requirement type="package" version="2022.6.15">ca-certificates</requirement> + <requirement type="package" version="2022.9.24">ca-certificates</requirement> <requirement type="package" version="16.02">p7zip</requirement> </requirements> </xml> <xml name="annotation"> <param argument="--annotated" type="boolean" truevalue="--annotated" falsevalue="" label="Only include genomes with annotation ?"/> </xml> - <xml name="dehydrated"> - <param argument="--dehydrated" type="boolean" truevalue="--dehydrated" falsevalue="" label="Download a dehydrated zip archive including the data report and locations of data files ?" help="Use the rehydrate tools to retrieve data files"/> - </xml> <xml name="assembly_level"> <param argument="--assembly-level" type="select" label="Restrict assemblies to a comma-separated list of one or more of these" multiple="true" optional="true"> <option value="chromosome">Chromosome</option> - <option value="complete_genome">Complete Genome</option> + <option value="complete">Complete Genome</option> <option value="contig">Contig</option> <option value="scaffold">Scaffold</option> </param> </xml> <xml name="assembly_source"> - <param argument="--assembly-source" type="select" optional="true"> + <param argument="--assembly-source" type="select" optional="true" label="Assembly source" help="Default (nothing selected) is both " > <option value="refseq">RefSeq</option> - <option value="genabnk">GenBank</option> + <option value="genbank">GenBank</option> </param> </xml> <xml name="text_or_file" token_what="accession" token_what_extended="NCBI Assembly accession" token_help="Can be NCBI Assembly or BioProject accession"> @@ -62,58 +59,47 @@ </sanitizer> </param> </xml> - <xml name="include" token_include_what="gbff" token_include_label="Include GenBank flat file sequence and annotation, if available"> - <param argument="--include-@INCLUDE_WHAT@" type="boolean" truevalue="--include-@INCLUDE_WHAT@" falsevalue="" label="@INCLUDE_LABEL@" /> - </xml> - <xml name="includes_genome"> - <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation, if available"/> - <expand macro="include" include_what="gtf" include_label="Include gtf annotation file, if available"/> - </xml> - <xml name="exclude" token_exclude_what="gff3" token_exclude_label="Exclude gff3 annotation file" token_checked="false"> - <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" truevalue="--exclude-@EXCLUDE_WHAT@" falsevalue="" label="@EXCLUDE_LABEL@" checked="@CHECKED@"/> - </xml> - <xml name="excludes_genome"> - <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/> - <expand macro="exclude" exclude_what="gff3" exclude_label="Exclude gff3 annotation file"/> - <expand macro="exclude" exclude_what="genomic-cds" exclude_label="Exclude cds from genomic sequence file"/> - <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/> - <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/> - </xml> - <xml name="excludes_gene"> - <expand macro="exclude" exclude_what="gene" exclude_label="Exclude gene sequence file"/> - <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/> - <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/> + <xml name="include"> + <param argument="--include" type="select" multiple="true" optional="true"> + <option value="genome" selected="true">genomic sequence (genome)</option> + <option value="rna">transcript (rna)</option> + <option value="protein">amnio acid sequences (protein)</option> + <option value="cds">nucleotide coding sequences (cds)</option> + <option value="gff3">general feature file (gff3)</option> + <option value="gtf">gene transfer format (gtf)</option> + <option value="gbff">GenBank flat file (gbff)</option> + <option value="seq-report">sequence report file (seq-report)</option> + </param> </xml> - <xml name="excludes_virus_protein"> - <yield/> - <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/> - <expand macro="exclude" exclude_what="pdb" exclude_label="Exclude protein structure files (pdb)"/> - <expand macro="exclude" exclude_what="gpff" exclude_label="Exclude protein sequence and annotation in GenPept flat file"/> - <expand macro="exclude" exclude_what="cds" exclude_label="Exclude CDS sequence file"/> - </xml> - <xml name="excludes_virus_genome"> - <expand macro="excludes_virus_protein"> - <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/> - </expand> - </xml> - <token name="@EXCLUDES_GENOME@">$file_choices.exclude_gff3 $file_choices.exclude_genomic_cds $file_choices.exclude_protein $file_choices.exclude_rna $file_choices.exclude_seq</token> - <token name="@EXCLUDES_GENE@">$exclude_gene $exclude_protein $exclude_rna</token> - <token name="@EXCLUDES_VIRUS_PROTEIN@">$exclude_protein $exclude_pdb $exclude_gpff $exclude_cds</token> - <token name="@EXCLUDES_VIRUS_GENOME@">$exclude_seq @EXCLUDES_VIRUS_PROTEIN@</token> - <xml name="includes_virus_genome"> - <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation"/> - </xml> - <token name="@INCLUDES_GENOME@">$file_choices.include_gbff $file_choices.include_gtf</token> - <token name="@INCLUDES_VIRUS_GENOME@">$include_gbff</token> + <token name="@INCLUDE@"><![CDATA[ + --include + #if $file_choices.include + #echo ",".join($file_choices.include) + #else + none + #end if + ]]></token> <xml name="released_options" token_released_what="genomes" token_before_or_after="before"> - <param argument="--released-@BEFORE_OR_AFTER@" type="text" optional="true" label="Only include @RELEASED_WHAT@ that have been released @BEFORE_OR_AFTER@ a specified date (MM/DD/YYYY)"></param> + <param argument="--released-@BEFORE_OR_AFTER@" type="text" optional="true" label="Only include @RELEASED_WHAT@ that have been released @BEFORE_OR_AFTER@ a specified date (MM/DD/YYYY)"> + <validator type="regex" message="enter a date in the form MM/DD/YYYY">[0-9]{2}/[0-9]{2}/[0-9]{4}</validator> + </param> </xml> <token name="@RELEASED_BEFORE@">#if $filters.released_before: --released-before '$filters.released_before' #end if </token> - <token name="@RELEASED_SINCE@">#if $filters.released_since: ---released-since '$filters.released_since' + <token name="@RELEASED_AFTER@">#if $filters.released_after: +--released-after '$filters.released_after' #end if </token> + + <xml name="genome_fasta_assert" tokens="el1,el2,expression" token_expression_n="1"> + <element name="@EL1@"> + <element name="@EL2@"> + <assert_contents> + <has_text_matching expression="@EXPRESSION@" n="@EXPRESSION_N@"/> + </assert_contents> + </element> + </element> + </xml> </macros>