Mercurial > repos > iuc > rnaquast
diff rna_quast.xml @ 0:33c060ec0ac9 draft
"planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
| author | iuc |
|---|---|
| date | Mon, 19 Oct 2020 08:04:52 +0000 |
| parents | |
| children | e989670c7fc7 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rna_quast.xml Mon Oct 19 08:04:52 2020 +0000 @@ -0,0 +1,332 @@ +<tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@"> + <description>A Quality Assessment Tool for De Novo Transcriptome Assemblies</description> + <macros> + <token name="@TOOL_VERSION@">2.1.0</token> + <xml name="element_matching_line" token_name="" token_expression=""> + <element name="@NAME@"> + <assert_contents><has_line_matching expression="@EXPRESSION@"/></assert_contents> + </element> + </xml> + <xml name="element_has_text" token_name="" token_text=""> + <element name="@NAME@"> + <assert_contents><has_text text="@TEXT@"/></assert_contents> + </element> + </xml> + + <xml name="details_output_test" token_assembler=""> + <element name="@ASSEMBLER@"> + <element name="5000%-assembled.list"><assert_contents><has_n_lines n="0"/></assert_contents></element> + <element name="9500%-assembled.list"><assert_contents><has_n_lines n="0"/></assert_contents></element> + <expand macro="element_matching_line" name="alignment_metrics" expression="\s*== ALIGNMENT METRICS \(calculated with reference genome but without gene database\) ==\s*"/> + <expand macro="element_matching_line" name="alignment_multiplicity" expression="unaligned=\d+ aligned=\d+ alignments=\d+\s*"/> + <expand macro="element_matching_line" name="alignments_per_isoform" expression="avg=[\d.]+\s*"/> + <expand macro="element_matching_line" name="basic_metrics" expression="\s*== BASIC TRANSCRIPTS METRICS \(calculated without reference genome and gene database\) ==\s*"/> + <expand macro="element_matching_line" name="block_length" expression="avg=[\d.]+\s*"/> + <expand macro="element_matching_line" name="blocks_per_alignment" expression="avg=[\d.]+\s+tot=\d+\s*"/> + <expand macro="element_matching_line" name="database_metrics" expression="\s*== GENE DATABASE METRICS ==\s*"/> + <expand macro="element_matching_line" name="misassemblies" expression="\s*== ALIGNMENT METRICS FOR MISASSEMBLED \(CHIMERIC\) TRANSCRIPTS \(calculated with reference genome or with gene database\) ==\s*"/> + <expand macro="element_matching_line" name="mismatch_rate" expression="avg=[\d.]+\s+tot=\d+\s*"/> + <expand macro="element_matching_line" name="sensitivity" expression="\s*== ASSEMBLY COMPLETENESS \(SENSITIVITY\) ==\s*"/> + <expand macro="element_matching_line" name="specificity" expression="\s*== ASSEMBLY SPECIFICITY ==\s*"/> + <expand macro="element_matching_line" name="transcript_length" expression="avg=[\d.]+\s*"/> + <expand macro="element_matching_line" name="x-aligned" expression="avg=[\d.]+\s*"/> + <expand macro="element_matching_line" name="x-assembled" expression="avg=[\d.]+\s*"/> + <expand macro="element_matching_line" name="x-assembled_exons" expression="avg=[\d.]+\s*"/> + <expand macro="element_matching_line" name="x-covered" expression="avg=[\d.]+\s*"/> + <expand macro="element_matching_line" name="x-covered_exons" expression="avg=[\d.]+\s*"/> + <expand macro="element_matching_line" name="x-matched" expression="avg=[\d.]+\s*"/> + <expand macro="element_matching_line" name="x-matched_blocks" expression="avg=[\d.]+\s*"/> + </element> + </xml> + + <xml name="txt_output_test" token_assembler=""> + <output name="short_report_txt"> + <assert_contents> + <has_text text="SHORT SUMMARY REPORT"/> + </assert_contents> + </output> + </xml> + <xml name="tex_output_test" token_assembler=""> + <output name="short_report_tex"> + <assert_contents> + <has_text text="Short summary report"/> + <has_text text="end{document}"/> + </assert_contents> + </output> + </xml> + <xml name="tsv_output_test" token_assembler=""> + <output name="short_report_tsv"> + <assert_contents> + <has_line_matching expression="^METRICS/TRANSCRIPTS\t.+$"/> + </assert_contents> + </output> + </xml> + <xml name="pdf_output_test" token_assembler=""> + <output name="short_report_pdf"> + <assert_contents> + <has_text text="rnaQUAST short report"/> + </assert_contents> + </output> + </xml> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">rnaquast</requirement> + </requirements> + <stdio> + <regex match="Traceback " source="both" level="fatal" description="rnaQuast failed" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + #import re + #for $i in $in_fasta + ln -s '$i' '${re.sub('[^\w\-.]', '_', i.element_identifier)}' && + #end for + #if $r + #for $rf in $r + ln -s '$rf' '${re.sub('[^\w\-.]', '_', rf.element_identifier)}' && + #end for + #end if + #if $gene_coordinates.use_gtf == "true" + #for $g in $gene_coordinates.gtf + ln -s '$g' '${re.sub('[^\w\-.]', '_', g.element_identifier)}' && + #end for + #end if + mkdir outputdir && + rnaQUAST.py + --threads \${GALAXY_SLOTS:-1} + --transcripts + #for $i in $in_fasta + '${re.sub('[^\w\-.]', '_', i.element_identifier)}' + #end for + $strand_specific + #if $r + -r + #for $rf in $r + '${re.sub('[^\w\-.]', '_', rf.element_identifier)}' + #end for + #end if + #if $gene_coordinates.use_gtf == "true" + --gtf + #for $g in $gene_coordinates.gtf + '${re.sub('[^\w\-.]', '_', g.element_identifier)}' + #end for + $gene_coordinates.disable_infer_genes + $gene_coordinates.disable_infer_transcripts + #end if + $prokaryote + --min_alignment '$min_alignment' + #if "pdf" not in $out_sr and "plots" not in $out_add + --no_plots + #end if + $blat + $busco_lineage + ##GeneMarkS-T is not available in conda $gene_mark + $meta + --lower_threshold $lower_threshold + --upper_threshold $upper_threshold + -o outputdir + + && mkdir details + + ## 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 + #set basename = os.path.splitext(re.sub('[^\w\-.]', '_', $i.element_identifier))[0] + && + (for f in \$(find 'outputdir/'$basename'_output' -type f); + do + d=\$(dirname \$f | cut -d"/" -f2 | cut -d'_' -f1) && + mv \$f details/"\$d"_____"\$(basename \$f | sed 's/$basename\.//')"; + done) + #end for + + ## rename .list files to .txt files to make them detectable (format detection by extension) + ## the final `true` seems needed since otherwise the `;` at the end is swallowed + && find details/ -name "*.list" -exec mv {} {}.txt \; + && 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" /> + <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> + <option value="false">No</option> + </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?"/> + </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 name="out_sr" type="select" multiple="true" label="Short report formats"> + <option value="tsv" selected="true">tabular</option> + <option value="txt">txt</option> + <option value="tex">tex</option> + <option value="pdf" selected="true">pdf</option> + </param> + <param name="out_add" type="select" multiple="true" label="Additional outputs"> + <option value="logs">Logs</option> + <option value="plots" selected="true">Plots (only for n>1)</option> + <option value="comparison" selected="true">Comparison for Chromosomes/scaffolds files (only for n>1)</option> + <option value="details" selected="true">Details per Chromosomes/scaffolds file</option> + <option value="details_plots" selected="true">Details per Chromosomes/scaffolds file as plot</option> + </param> + </inputs> + + <outputs> + <data name="short_report_pdf" format="pdf" label="${tool.name} on ${on_string}: pdf report" from_work_dir="outputdir/short_report.pdf"> + <filter>"pdf" in out_sr</filter> + </data> + <data name="short_report_txt" format="txt" label="${tool.name} on ${on_string}: txt report" from_work_dir="outputdir/short_report.txt"> + <filter>"txt" in out_sr</filter> + </data> + <data name="short_report_tex" format="txt" label="${tool.name} on ${on_string}: tex report" from_work_dir="outputdir/short_report.tex"> + <filter>"tex" in out_sr</filter> + </data> + <data name="short_report_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv report" from_work_dir="outputdir/short_report.tsv"> + <filter>"tsv" in out_sr</filter> + </data> + <collection name="list_logs" type="list" label="${tool.name} on ${on_string}: logs" > + <discover_datasets ext="txt" pattern="(?P<name>.+)\.log" directory="outputdir/logs/" visible="false" /> + <filter>"logs" in out_add</filter> + </collection> + <!-- note the output filter of the next two outputs checks if there is + more than 1 input for in_fasta (for 1 its a HDA, for more list or HDAs) --> + <collection name="comparison_png" type="list" label="${tool.name} on ${on_string}: comparison plots" > + <discover_datasets ext="png" pattern="(?P<name>.+)\.png" directory="outputdir/comparison_output/" visible="false" recurse="true"/> + <filter> isinstance(in_fasta, list) and "plots" in out_add</filter> + </collection> + <collection name="comparison" type="list" label="${tool.name} on ${on_string}: comparison" > + <discover_datasets ext="txt" pattern="(?P<name>.+)\.txt" directory="outputdir/comparison_output/" visible="false" recurse="true" /> + <filter> isinstance(in_fasta, list) and "comparison" in out_add</filter> + </collection> + <collection name="details" type="list:list" label="${tool.name} on ${on_string}: detailed output"> + <discover_datasets pattern="(?P<identifier_0>.+)_____(?P<identifier_1>.+)\.(?P<ext>txt)" directory="details/" visible="false"/> + <filter>"details" in out_add</filter> + </collection> + <collection name="details_png" type="list:list" label="${tool.name} on ${on_string}: detailed output plots"> + <discover_datasets pattern="(?P<identifier_0>.+)_____(?P<identifier_1>.+)\.(?P<ext>png)" directory="details/" visible="false"/> + <filter>"details_plots" in out_add</filter> + </collection> + </outputs> + <tests> + <test expect_num_outputs="7"> + <param name="in_fasta" 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" /> + <param name="gtf" value="Saccharomyces_cerevisiae.R64-1-1.75.gtf" ftype="gtf" /> + <param name="disable_infer_genes" value="true"/> + <param name="disable_infer_transcripts" value="true"/> + </conditional> + <param name="out_sr" value="txt,tex,tsv" /> + <param name="out_add" value="logs,comparison,plots,details" /> + <expand macro="txt_output_test"/> + <expand macro="tex_output_test"/> + <expand macro="tsv_output_test"/> + <output_collection name="comparison_png" type="list" count="15"/> + <output_collection name="comparison" type="list" count="19"/> + <output_collection name="list_logs" type="list" count="8"/> + <output_collection name="details" type="list:list" count="2"> + <expand macro="details_output_test" assembler="Trinity"/> + <expand macro="details_output_test" assembler="idba"/> + </output_collection> + </test> + <test expect_num_outputs="6"> + <param name="in_fasta" 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" /> + + <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> + </test> + </tests> + <help><![CDATA[ +**What is rnaQUAST** +- a quality assessment tool for de novo transcriptome assemblies +- evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database +- calculates various metrics that demonstrate completeness and correctness levels of the assembled transcripts + +**Using rnaQuast without reference** you wont get: + +- x-assembled (Exons) +- Alignments per Isoform +- x-covered (Exons) +- x-matched (Blocks) +- gmap build logs + +**Using rnaQuast with reference** you will get: +- Reports +- Logs +- Alignement/Basic Metrics +- Misassemblies/ Specificity/ Sensitivity +- Alignment multiplicity +- Block/ Transcript Lentgh +- Blocks per alignment +- Mismatch rate +- x-aligned +- Nx +- Blocks per alignment +- gmap build logs + +**Using rnaQuast without gene coordinates** you wont get: +- x-assembled (Exons) +- Alignments per Isoform +- x-covered (Exons) +- x-matched (Blocks) +- gmap build logs +- Database Metrics +- Alignment multiplicity +- Mismatch rate +- NAx +- x-aligned +**Using rnaQuast with gene coordinates** you will get: +- Reports +- Logs +- Alignement/Basic Metrics +- Misassemblies/Specificity/Sensitivity +- Alignment multiplicity +- Block/Transcript length +- Blocks per alignment +- Mismatch rate +- x-aligned +- Nx/NAx +- gmap build logs +- Database Metrics +- Alignment multiplicity +More informations, see citations. + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btw218 </citation> + </citations> +</tool>