Mercurial > repos > iuc > rnaquast
changeset 9:3967889cda03 draft default tip
planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 4591c0ac5cf45b54e9fadb5d196ec3376b5b926f
| author | iuc |
|---|---|
| date | Thu, 17 Jul 2025 16:37:52 +0000 |
| parents | f73ab5187eed |
| children | |
| files | macros.xml rna_quast.xml |
| diffstat | 2 files changed, 33 insertions(+), 19 deletions(-) [+] |
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--- a/macros.xml Fri Aug 30 14:12:04 2024 +0000 +++ b/macros.xml Thu Jul 17 16:37:52 2025 +0000 @@ -12,6 +12,6 @@ </xrefs> </xml> <token name="@TOOL_VERSION@">2.3.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">20.05</token> </macros> \ No newline at end of file
--- a/rna_quast.xml Fri Aug 30 14:12:04 2024 +0000 +++ b/rna_quast.xml Thu Jul 17 16:37:52 2025 +0000 @@ -27,14 +27,14 @@ #end if mkdir outputdir && rnaQUAST.py - --threads \${GALAXY_SLOTS:-8} + --threads "\${GALAXY_SLOTS:-8}" --transcripts #for $i in $transcripts '${re.sub('[^\w.]', '_', i.element_identifier)}' #end for #if $reads_option.selector == 'paired' - --left_reads '${reads_option.forward_reads}' - --right_reads '${reads_option.reverse_reads}' + --left_reads '${reads_option.paired_reads.forward}' + --right_reads '${reads_option.paired_reads.reverse}' #else if $reads_option.selector == 'single' --single_reads '${reads_option.single_reads}' #end if @@ -117,17 +117,16 @@ <param argument="--transcripts" type="data" format="fasta" multiple="true" label="Transcripts" help="File(s) with transcripts in FASTA format."/> <conditional name="reads_option"> <param name="selector" type="select" label="Single-end or paired-end reads"> - <option value="" selected="true">Disabled-end</option> + <option value="" selected="true">Disabled</option> <option value="single" selected="true">Single-end</option> <option value="paired">Paired-end (as individual datasets)</option> </param> <when value=""/> <when value="single"> - <param format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" name="single_reads" type="data" label="RNA-Seq FASTQ/FASTA file"/> + <param format="fastqsanger,fastqsanger.gz" name="single_reads" type="data" label="RNA-Seq FASTQ file"/> </when> <when value="paired"> - <param name="forward_reads" format="fastq,fastq.gz,fastqsanger ,fastqsanger.gz" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/> - <param name="reverse_reads" format="fastq,fastq.gz,fastqsanger, fastqsanger.gz" type="data" label="RNA-Seq FASTQ/FASTA file, reverse reads"/> + <param name="paired_reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Paired RNA-Seq FASTQ data"/> </when> </conditional> <param argument="--reference" type="data" format="fasta" label="Reference genome" multiple="true" optional="true" help="File with reference genome containing all chromosomes/scaffolds in FASTA forma." /> @@ -269,8 +268,7 @@ <param name="out_sr" value="tabular"/> </section> <conditional name="reads_option"> - <param name="selector" value="single"/> - <param name="single_reads" value=""/> + <param name="selector" value=""/> </conditional> <output name="short_report_tabular" file="test_03_short_report.tab"/> </test> @@ -307,8 +305,12 @@ </section> <conditional name="reads_option"> <param name="selector" value='paired'/> - <param name="forward_reads" value="input_F.fastqsanger"/> - <param name="reverse_reads" value="input_F.fastqsanger"/> + <param name="paired_reads"> + <collection type="paired"> + <element name="forward" value="input_F.fastqsanger" ftype="fastqsanger"/> + <element name="reverse" value="input_F.fastqsanger" ftype="fastqsanger"/> + </collection> + </param> </conditional> <output name="short_report_tabular"> <assert_contents> @@ -326,8 +328,12 @@ </conditional> <conditional name="reads_option"> <param name="selector" value='paired'/> - <param name="forward_reads" value="input_F.fastqsanger"/> - <param name="reverse_reads" value="input_R.fastqsanger"/> + <param name="paired_reads"> + <collection type="paired"> + <element name="forward" value="input_F.fastqsanger" ftype="fastqsanger"/> + <element name="reverse" value="input_R.fastqsanger" ftype="fastqsanger"/> + </collection> + </param> </conditional> <section name="output_options"> <param name="out_sr" value="tabular"/> @@ -356,8 +362,12 @@ <param name="reference" value="reference.fasta"/> <conditional name="reads_option"> <param name="selector" value='paired'/> - <param name="forward_reads" value="input_F.fastqsanger"/> - <param name="reverse_reads" value="input_R.fastqsanger"/> + <param name="paired_reads"> + <collection type="paired"> + <element name="forward" value="input_F.fastqsanger" ftype="fastqsanger"/> + <element name="reverse" value="input_R.fastqsanger" ftype="fastqsanger"/> + </collection> + </param> </conditional> <conditional name="use_busco"> <param name="selector" value="true"/> @@ -366,7 +376,7 @@ <param name="cached_db" value="busco-demo-db-20230328"/> </conditional> </conditional> - <section name="output_options"> + <section name="output_options"> <param name="out_sr" value="pdf,tabular"/> <param name="out_add" value="fasta,gz"/> </section> @@ -401,7 +411,9 @@ <param name="cached_db" value="busco-demo-db-20230328"/> </conditional> </conditional> - <param name="out_add" value="complete,fasta,logs,gz"/> + <section name="output_options"> + <param name="out_add" value="complete,fasta,logs,gz"/> + </section> <conditional name="reads_option"> <param name="selector" value="single"/> <param name="single_reads" value="single_end.fastq.gz"/> @@ -450,7 +462,9 @@ <param name="cached_db" value="busco-demo-db-20230328"/> </conditional> </conditional> - <param name="out_add" value="complete,fasta,logs,gz"/> + <section name="output_options"> + <param name="out_add" value="complete,fasta,logs,gz"/> + </section> <conditional name="reads_option"> <param name="selector" value="single"/> <param name="single_reads" value="single_end.fastq.gz"/>