Mercurial > repos > iuc > find_nested_alt_orfs
diff find_nested_alt_orfs.xml @ 0:14f4c7a8a962 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
| author | iuc |
|---|---|
| date | Mon, 11 Apr 2022 20:37:19 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/find_nested_alt_orfs.xml Mon Apr 11 20:37:19 2022 +0000 @@ -0,0 +1,115 @@ +<tool id="find_nested_alt_orfs" name="Find Nested Alternate ORFs (nAlt-ORFs)" version="@TOOL_VERSION@" profile="20.05"> + <description>from BED and 2bit/FASTA</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edam_ontology"/> + <expand macro="requirements"> + <requirement type="package" version="377">ucsc-fatotwobit</requirement> + </expand> + <version_command>find_nested_alt_orfs.py --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + #if $ref.ref_source == 'history': + #if $ref.ref_file.is_of_type('fasta'): + #set $twobit_filename = "out.2bit" + faToTwoBit '${ref.ref_file}' '$twobit_filename' -stripVersion && + #else: + #set $twobit_filename = $ref.ref_file + #end if + #else: + #set $twobit_filename = $ref.ref_loc.fields.path + #end if + find_nested_alt_orfs.py + --twobit '$twobit_filename' + + --min_length '$min_length' + + --reference '${input.metadata.dbkey}' + + --bed '$input' + + #if $no_canonical_cds: + --no_canonical_cds '$no_canonical_cds' + #end if + + --translation_table '$translation_table' + + --bed_out '$bed_out' + + --peptide_fasta_out '$peptide_fasta_out' + + --naltorfs_fasta_out '$naltorfs_fasta_out' + + --cds_fasta_out '$cds_fasta_out' + + $unique_sequences + + #if $write_log: + --log '$log' + #end if + ]]></command> + <inputs> + <param argument="--bed" name="input" type="data" format="bed" label="Gene BED" help="A BED file with 12 columns"/> + <conditional name="ref"> + <param name="ref_source" type="select" label="Source for Genomic Sequence Data"> + <option value="cached">Locally cached genome</option> + <option value="history">History dataset genome</option> + </param> + <when value="cached"> + <param argument="--twobit" name="ref_loc" type="select" label="Select reference genome"> + <options from_data_table="twobit"/> + </param> + </when> + <when value="history"> + <param argument="--twobit" name="ref_file" type="data" format="twobit,fasta" label="Reference genome"/> + </when> + </conditional> + <param argument="--min_length" type="integer" value="150" min="1" label="Minimum length of peptide translation to report"/> + <param argument="--unique_sequences" type="boolean" truevalue="--unique_sequences" falsevalue="" checked="True" label="Only report the first unique occurrence of an alternate sequence"/> + <param argument="--no_canonical_cds" type="data" format="bed" optional="True" label="Do not report any alternate sequences that match a provided canonical CDS" help="A BED file with 12 columns"/> + <expand macro="translation_table_select_parameter"/> + <param name="write_log" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Create log file"/> + </inputs> + <outputs> + <data name="bed_out" format="bed" label="Find Nested nAlt-ORFs on ${on_string}: nAlt-ORFs.proBed"> + <actions> + <action name="column_names" type="metadata" default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts,proteinAccession,peptideSequence,uniqueness,genomeReferenceVersion,psmScore,fdr,modifications,charge,expMassToCharge,calcMassToCharge,psmRank,datasetID,uri"/> + </actions> + </data> + <data name="peptide_fasta_out" format="fasta" label="Find nAlt-ORFs on ${on_string}: peptide.fasta"/> + <data name="naltorfs_fasta_out" format="fasta" label="Find nAlt-ORFs on ${on_string}: nAlt-ORFs.fasta"/> + <data name="cds_fasta_out" format="fasta" label="Find nAlt-ORFs on ${on_string}: canonical CDS.fasta"/> + <data name="log" format="txt" label="Find nAlt-ORFs on ${on_string}: log.txt"> + <filter>write_log</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" value="gencode_canonical.hg38.chr6_GL0002508.bed" dbkey="hg38" ftype="bed12"/> + <conditional name="ref"> + <param name="ref_source" value="history"/> + <param name="ref_file" value="hg38.chr6_GL000250v2_alt.2bit.gz" dbkey="hg38" ftype="twobit"/> + </conditional> + <param name="min_length" value="150"/> + <param name="unique_sequences" value="true"/> + <param name="no_canonical_cds" value="gencode_canonical.hg38.chr6_GL0002508.bed" dbkey="hg38" ftype="bed12"/> + <param name="translation_table" value="1"/> + <param name="write_log" value="true"/> + <output name="bed_out" value="bed_out.bed"/> + <output name="peptide_fasta_out" value="peptide_fasta_out.fasta"/> + <output name="naltorfs_fasta_out" value="naltorfs_fasta_out.fasta"/> + <output name="cds_fasta_out" value="cds_fasta_out.fasta"/> + <output name="log" value="find_naltorfs_log.txt"/> + </test> + </tests> + <help><![CDATA[ +Find Nested Alternate Open Reading Frames (nAlt-ORFs). + +Using a BED12 file containing the location of genes, and a matching reference genome, +this tool searches in the alternate reading frames of the provided canonical coding sequence, +and outputs nested alternate ORFs which match the provided thresholds. + +Translation table identifiers are based upon NCBI standards (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi). + ]]></help> + <expand macro="citations"/> +</tool>