Mercurial > repos > iuc > rnaquast
changeset 3:a9edbe21bf47 draft
"planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
| author | iuc |
|---|---|
| date | Fri, 14 Jan 2022 18:42:15 +0000 |
| parents | 96f74538896e |
| children | f9f2ad782d8f |
| files | rna_quast.xml |
| diffstat | 1 files changed, 78 insertions(+), 25 deletions(-) [+] |
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--- a/rna_quast.xml Tue Oct 19 11:02:19 2021 +0000 +++ b/rna_quast.xml Fri Jan 14 18:42:15 2022 +0000 @@ -1,10 +1,11 @@ -<tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@"> - <description>A Quality Assessment Tool for De Novo Transcriptome Assemblies</description> +<tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description>A quality assessment tool for De Novo transcriptome assemblies</description> <xrefs> <xref type="bio.tools">rnaQUAST</xref> </xrefs> <macros> <token name="@TOOL_VERSION@">2.2.1</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="element_matching_line" token_name="" token_expression=""> <element name="@NAME@"> <assert_contents> @@ -92,7 +93,7 @@ </stdio> <command detect_errors="exit_code"><![CDATA[ #import re - #for $i in $in_fasta + #for $i in $transcripts ln -s '$i' '${re.sub('[^\w\-.]', '_', i.element_identifier)}' && #end for #if $r @@ -109,7 +110,7 @@ rnaQUAST.py --threads \${GALAXY_SLOTS:-1} --transcripts - #for $i in $in_fasta + #for $i in $transcripts '${re.sub('[^\w\-.]', '_', i.element_identifier)}' #end for $strand_specific @@ -133,8 +134,10 @@ --no_plots #end if $blat - $busco_lineage - ##GeneMarkS-T is not available in conda $gene_mark + #if $busco_option.busco == 'true' + --busco $busco_option.lineage + #end if + ##$gene_mark $meta --lower_threshold $lower_threshold --upper_threshold $upper_threshold @@ -145,7 +148,7 @@ ## move per outputs that are generated for each input (outputdir/ASSEMBLER_output) ## to a joint dir (details) to make them discoverable ## also remove "ASSEMBLER." prefixes from files (otherwise the test macros don't work) - #for $i in $in_fasta + #for $i in $transcripts #set basename = os.path.splitext(re.sub('[^\w\-.]', '_', $i.element_identifier))[0] && (for f in \$(find 'outputdir/'$basename'_output' -type f); @@ -161,9 +164,10 @@ && true ]]> </command> <inputs> - <param name="in_fasta" type="data" format="fasta" multiple="true" label="Chromosomes/scaffolds file" /> - <param name="strand_specific" argument="-ss" type="boolean" truevalue="-ss" falsevalue="" checked="false" label="Strand-specific" /> - <param name="r" optional="true" argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" /> + <param argument="--transcripts" type="data" format="fasta" multiple="true" label="Transcripts" help="File(s) with transcripts in FASTA format."/> + <param name="strand_specific" argument="-ss" type="boolean" truevalue="-ss" falsevalue="" checked="false" label="Strand-specific" + help="Set if transcripts were assembled using strand-specific RNA-Seq data in order to benefit from knowing whether the transcript originated from the + or - strand"/> + <param name="r" optional="true" argument="-r" type="data" format="fasta" multiple="true" label="Reference genome" help="File with reference genome containing all chromosomes/scaffolds in FASTA forma." /> <conditional name="gene_coordinates"> <param name="use_gtf" type="select" label="Use file with gene coordinates in GTF/GFF format?" help="We recommend to use files downloaded from GENCODE or Ensembl."> <option value="true" selected="true">Yes</option> @@ -171,20 +175,37 @@ </param> <when value="true"> <param name="gtf" argument="--gtf" type="data" format="gtf,gff,gff3" multiple="true" label="GTF/GFF file" /> - <param argument="--disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="false" label=" GTF file contains genes records?" /> - <param argument="--disable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="false" label="GTF file contains transcripts records?" /> + <param argument="--disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="false" label=" GTF file contains genes records?" + help="Use this option if your GTF file already contains genes records, otherwise gffutils will fix it. Note that gffutils may work for quite a long time"/> + <param argument="--disable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="false" label="GTF file contains transcripts records?" help="Is option if your GTF file already contains transcripts records, otherwise gffutils will fix it."/> </when> <when value="false"> </when> </conditional> - <param argument="--prokaryote" type="boolean" truevalue="--prokaryote" falsevalue="" checked="false" label="Is genome prokararyotic?" /> - <param argument="--min_alignment" type="integer" value="50" label="Minimal alignment length to be used" /> - <param argument="--blat" type="boolean" truevalue="--blat" falsevalue="" checked="false" label="Run with BLAT alignment tool instead of GMAP?" /> - <param argument="--busco_lineage" type="boolean" truevalue="--busco_lineage" falsevalue="" checked="false" label="Run BUSCO tool?" help="The BUSCO tool detects core genes in the assembly. Use this option to provide path to the BUSCO lineage data (Eukaryota, Metazoa, Arthropoda, Vertebrata or Fungi)." /> - <!-- GeneMarkS-T is not available in conda <param argument="\-\-gene_mark" type="boolean" truevalue="\-\-gene_mark" falsevalue="" checked="false" label="Run with GeneMarkS-T gene prediction tool?"/>--> - <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Meta Transcriptome" help="Run quality asessment for Meta Transcriptome" /> - <param argument="--lower_threshold" type="integer" value="50" label="Lower threshold for x_assembled/covered/matched metrics." /> - <param argument="--upper_threshold" type="integer" value="95" label="Upper threshold for x_assembled/covered/matched metrics." /> + <param argument="--prokaryote" type="boolean" truevalue="--prokaryote" falsevalue="" checked="false" label="Is genome prokararyotic?" help="Use this option if the genome is prokaryotic."/> + <param argument="--min_alignment" type="integer" value="50" label="Minimal alignment length to be used" help="Default value is 50"/> + <param argument="--blat" type="boolean" truevalue="--blat" falsevalue="" checked="false" label="Run with BLAT alignment tool instead of GMAP?" help="Blat is especially useful for aligning long sequences and gapped mapping, which cannot be performed properly by other fast sequence mappers designed for short reads. " /> + <conditional name="busco_option"> + <param argument="--busco" type="select" label="Run BUSCO tool?" help="BUSCO allows to detect core genes in the assembled transcripts"> + <option value="false">Disabled</option> + <option value="true">Enabled</option> + </param> + <when value="false"/> + <when value="true"> + <param name="lineage" type="select" label="Lineage" help="Select a lineage for using BUSCO"> + <option value="metazoa">Metazoa</option> + <option value="eukaryota">Eukaryota</option> + <option value="arthropoda">Arthropoda</option> + <option value="vertebrata">Vertebrata</option> + <option value="fungi">Fungi</option> + <option value="bacteria">Bacteria</option> + </param> + </when> + </conditional> + <!--param argument="-\-gene_mark" type="boolean" truevalue="-\-gene_mark" falsevalue="" checked="false" label="Run with GeneMarkS-T gene prediction tool?" help="GeneMarkS-T allows to predict genes in the assembled transcripts without reference genome"/--> + <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Meta Transcriptome" help="Run quality asessment for meta-transcriptome assemblies" /> + <param argument="--lower_threshold" type="integer" value="50" label="Lower threshold for x-assembled/covered/matched metrics." /> + <param argument="--upper_threshold" type="integer" value="95" label="Upper threshold for x-assembled/covered/matched metrics." /> <param name="out_sr" type="select" multiple="true" label="Short report formats"> <option value="tsv" selected="true">tabular</option> <option value="txt">txt</option> @@ -218,14 +239,14 @@ <filter>"logs" in out_add</filter> </collection> <!-- note the output filter of the next two outputs checks if there is - more than 1 input for in_fasta (for 1 its a HDA, for more list or HDAs) --> + more than 1 input for transcripts (for 1 its a HDA, for more list or HDAs) --> <collection name="comparison_png" type="list" label="${tool.name} on ${on_string}: comparison plots"> <discover_datasets ext="png" pattern="(?P<name>.+)\.png" directory="outputdir/comparison_output/" visible="false" recurse="true" /> - <filter> isinstance(in_fasta, list) and "plots" in out_add</filter> + <filter> isinstance(transcripts, list) and "plots" in out_add</filter> </collection> <collection name="comparison" type="list" label="${tool.name} on ${on_string}: comparison"> <discover_datasets ext="txt" pattern="(?P<name>.+)\.txt" directory="outputdir/comparison_output/" visible="false" recurse="true" /> - <filter> isinstance(in_fasta, list) and "comparison" in out_add</filter> + <filter> isinstance(transcripts, list) and "comparison" in out_add</filter> </collection> <collection name="details" type="list:list" label="${tool.name} on ${on_string}: detailed output"> <discover_datasets pattern="(?P<identifier_0>.+)_____(?P<identifier_1>.+)\.(?P<ext>txt)" directory="details/" visible="false" /> @@ -238,7 +259,7 @@ </outputs> <tests> <test expect_num_outputs="7"> - <param name="in_fasta" value="idba.fasta,Trinity.fasta" ftype="fasta" /> + <param name="transcripts" value="idba.fasta,Trinity.fasta" ftype="fasta" /> <param name="r" value="Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa" ftype="fasta" /> <conditional name="gene_coordinates"> <param name="use_gtf" value="true" /> @@ -260,7 +281,7 @@ </output_collection> </test> <test expect_num_outputs="6"> - <param name="in_fasta" value="Trinity.fasta" ftype="fasta" /> + <param name="transcripts" value="Trinity.fasta" ftype="fasta" /> <conditional name="gene_coordinates"> <param name="use_gtf" value="false" /> </conditional> @@ -285,6 +306,38 @@ </element> </output_collection> </test> + <test expect_num_outputs="6"> + <param name="transcripts" value="Trinity.fasta" ftype="fasta" /> + <conditional name="gene_coordinates"> + <param name="use_gtf" value="false" /> + </conditional> + <param name="min_alignment" value="30" /> + <param name="lower_threshold" value="45" /> + <param name="upper_threshold" value="95" /> + <param name="out_sr" value="txt,tex,tsv,pdf" /> + <param name="out_add" value="logs,details_plots" /> + <conditional name="busco_option"> + <param name="busco" value="true"/> + <param name="lineage" value="metazoa"/> + </conditional> + <expand macro="pdf_output_test" /> + <expand macro="tex_output_test" /> + <expand macro="tsv_output_test" /> + <expand macro="txt_output_test" /> + <output_collection name="list_logs" type="list"> + <expand macro="element_has_text" name="Trinity.GeneMarkS_T.err" text="" /> + <expand macro="element_matching_line" name="rnaQUAST" expression="Thank you for using rnaQUAST!" /> + </output_collection> + <output_collection name="details_png" type="list:list" count="1"> + <element name="Trinity"> + <expand macro="element_has_text" name="Nx" text="PNG" /> + <expand macro="element_has_text" name="transcript_length" text="PNG" /> + </element> + </output_collection> + <assert_command> + <has_text text="--busco metazoa"/> + </assert_command> + </test> </tests> <help><![CDATA[ **What is rnaQUAST**