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author | enios |
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date | Sat, 22 May 2021 07:35:58 +0000 |
parents | 11d232ed904c |
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<tool id="gffcompare" name="GffCompare"> <description>compare assembled transcripts to a reference annotation</description> <requirements> <container type="docker">bianca7/lncrna:gffcompare</container> </requirements> <!--version_command>gffcompare -v | awk '{print $2}'</version_command--> <command detect_errors="aggressive"><![CDATA[ #import re #set escaped_element_identifiers = [re.sub('[^\w\-]', '_', str(_.element_identifier)) for _ in $gffinputs] #for $input, $escaped_element_identifier in zip($gffinputs, $escaped_element_identifiers): ln -s '$input' '$escaped_element_identifier' && #end for #if $seq_data.use_seq_data == "Yes": #if $seq_data.seq_source.index_source == "history": ln -s '$seq_data.seq_source.ref_file' ref_seq.fa && #else: ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa && #end if #end if #if $annotation.use_ref_annotation == "Yes": #if $annotation.ref_source.ref_source_sel == "history": ln -s '$annotation.ref_source.reference_annotation' ref_annotation && #else ln -s '$annotation.ref_source.index.fields.path' ref_annotation && #end if #end if gffcompare ## Use annotation reference? #if $annotation.use_ref_annotation == "Yes": -r ref_annotation $annotation.ignore_nonoverlapping_reference $annotation.ignore_nonoverlapping_transfrags $annotation.strict_match #end if #if $annotation.refmap_tmap == "": -T #end if ## Use sequence data? #if $seq_data.use_seq_data == "Yes": -s ref_seq.fa #end if $discard_single_exon $discard_duplicates $no_merge -e $max_dist_exon -d $max_dist_group $chr_stats -p '$adv_output.p' $adv_output.A $adv_output.C $adv_output.X $adv_output.K #for $escaped_element_identifier in $escaped_element_identifiers: '$escaped_element_identifier' #end for ]]></command> <inputs> <param format="gtf" name="gffinputs" type="data" label="GTF inputs for comparison" help="" multiple="true" /> <conditional name="annotation"> <param label="Use Reference Annotation" name="use_ref_annotation" type="select"> <option value="No">No</option> <option value="Yes">Yes</option> </param> <when value="Yes"> <conditional name="ref_source"> <param label="Choose the source for the reference annotation" name="ref_source_sel" type="select"> <option value="cached">Locally cached</option> <option value="history">History</option> </param> <when value="cached"> <param argument="-r" label="Using reference annotation" name="index" type="select"> <options from_data_table="gene_sets"> <!--filter column="dbkey" key="dbkey" ref="gffinputs" type="data_meta" /--> </options> <validator message="No reference annotation is available for the build associated with the selected input dataset" type="no_options" /> </param> </when> <when value="history"> <param argument="-r" format="gff3,gtf" help="Requires an annotation file in GFF3 or GTF format." label="Reference Annotation" name="reference_annotation" type="data" /> </when> </conditional> <param argument="-R" falsevalue="" help="consider only the reference transcripts that overlap any of the input transfrags (Sn correction)" label="Ignore reference transcripts that are not overlapped by any input transfrags" name="ignore_nonoverlapping_reference" truevalue="-R" type="boolean" /> <param argument="-Q" falsevalue="" help="consider only the input transcripts that overlap any of the reference transcripts (Sp correction). Warning: this will discard all 'novel' loci!" label="Ignore input transcripts that are not overlapped by any reference transcripts" name="ignore_nonoverlapping_transfrags" truevalue="-Q" type="boolean" /> <param argument="--strict-match" name="strict_match" type="boolean" checked="false" truevalue="--strict-match" falsevalue="" label="the match code '=' is only assigned when all exon boundaries match" help="code '~' is assigned for intron chain match or single-exon" /> <param argument="-T" name="refmap_tmap" label="Generate tmap or refmap file for each input file" type="select" multiple="True"> <option value="refmap" selected="True">refmap</option> <option value="tmap" selected="True">tmap</option> </param> </when> <when value="No"> <param argument="-T" name="refmap_tmap" label="Generate tmap file for each input file" type="select" multiple="True"> <option value="tmap" selected="True">tmap</option> </param> </when> </conditional> <conditional name="seq_data"> <param help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff." label="Use Sequence Data" name="use_seq_data" type="select"> <option value="No">No</option> <option value="Yes">Yes</option> </param> <when value="No"/> <when value="Yes"> <conditional name="seq_source"> <param label="Choose the source for the reference sequence" name="index_source" type="select"> <option value="cached">Locally cached</option> <option value="history">History</option> </param> <when value="cached"> <param argument="-s" label="Using reference genome" name="index" type="select"> <options from_data_table="fasta_indexes"> <filter column="dbkey" key="dbkey" ref="gffinputs" type="data_meta" /> </options> <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> </param> </when> <when value="history"> <param argument="-s" format="fasta" label="Using reference file" name="ref_file" type="data" /> </when> </conditional> </when> </conditional> <param name="discard_single_exon" argument="-M/-N" type="select" label="Discard single-exon transcripts" help="If -S and also --strict-match is given, exact matching of all exon boundaries is required"> <option selected="True" value="">No</option> <option value="-M">Discard single-exon transfrags and reference transcripts</option> <option value="-N">Discard single-exon reference transcripts</option> </param> <param label="Discard duplicates" name="discard_duplicates" type="select"> <option value="">None</option> <option value="-D">discard 'duplicate' query transfrags within a single sample (-D)</option> <option value="-S">Only discard 'duplicate' query or reference transcripts if their boundaries are fully contained within other, larger or identical transfrags (-S)</option> </param> <param name="no_merge" argument="--no-merge" type="boolean" checked="false" truevalue="--no-merge" falsevalue="" label="Disable close-exon merging" help="Default: merge exons separated by 'introns' shorter than 5 bases" /> <param argument="-e" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" label="Max. Distance for assessing exon accuracy" name="max_dist_exon" type="integer" value="100" /> <param argument="-d" help="max. distance (range) for grouping transcript start sites. Default: 100" label="Max distance for transcript grouping" name="max_dist_group" type="integer" value="100" /> <param name="chr_stats" argument="--chr-stats" type="boolean" checked="false" truevalue="--chr-stats" falsevalue="" label="Show summary and accuracy data separately for each reference sequence in the transcript accuracy data set" /> <section name="adv_output" title="Options for the combined GTF output file"> <param argument="-p" type="text" value="TCONS" label="name prefix for consensus transcripts" help="for combined.gtf" /> <param argument="-C" type="boolean" checked="false" truevalue="-C" falsevalue="" label="discard matching and 'contained' transfrags" help="i.e. collapse intron-redundant transfrags across all query files" /> <param argument="-A" type="boolean" checked="false" truevalue="-A" falsevalue="" label="discard the 'contained' transfrags except intron-redundant transfrags starting with a different 5' exon" help="like -C but does not discard intron-redundant transfrags if they start with a different 5' exon" /> <param argument="-X" type="boolean" checked="false" truevalue="-X" falsevalue="" label="discard the 'contained' transfrags also if ends stick out within the container's introns" help="like -C but also discard contained transfrags if transfrag ends stick out within the container's introns" /> <param argument="-K" type="boolean" checked="false" truevalue="-K" falsevalue="" label="do NOT discard any redundant transfrag matching a reference" help="for -C/-A/-X" /> </section> </inputs> <outputs> <data format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: transcript accuracy" name="transcripts_stats" /> <data format="tabular" from_work_dir="gffcmp.loci" label="${tool.name} on ${on_string}: loci" name="transcripts_loci" /> <data format="tabular" from_work_dir="gffcmp.tracking" label="${tool.name} on ${on_string}: data ${gffinputs[0].hid} tracking file" name="transcripts_tracking" /> <data format="gtf" from_work_dir="gffcmp.combined.gtf" label="${tool.name} on ${on_string}: combined transcripts" name="transcripts_combined"> <filter>(isinstance(gffinputs, list) and len(gffinputs) > 1) or annotation['use_ref_annotation'] == "No"</filter> </data> <data format="gtf" from_work_dir="gffcmp.annotated.gtf" label="${tool.name} on ${on_string}: annotated transcripts" name="transcripts_annotated"> <filter>not (isinstance(gffinputs, list) and len(gffinputs) > 1) and annotation['use_ref_annotation'] == "Yes"</filter> </data> <collection name="refmap_output" type="list" label="${tool.name} on ${on_string}: refmap"> <discover_datasets pattern="gffcmp\.(?P<designation>.+)\.refmap" ext="tabular" /> <filter>annotation['refmap_tmap'] != None and 'refmap' in annotation['refmap_tmap']</filter> </collection> <collection name="tmap_output" type="list" label="${tool.name} on ${on_string}: tmap"> <discover_datasets pattern="gffcmp\.(?P<designation>.+)\.tmap" ext="tabular" /> <filter>annotation['refmap_tmap'] != None and 'tmap' in annotation['refmap_tmap']</filter> </collection> </outputs> <citations> <citation type="doi">10.1038/nbt.1621</citation> </citations> </tool>