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diff gffcompare.xml @ 16:24d0a81802d6 draft
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| author | enios |
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| date | Sat, 22 May 2021 07:30:49 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gffcompare.xml Sat May 22 07:30:49 2021 +0000 @@ -0,0 +1,499 @@ +<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 ${on_string}: tmap"> + <discover_datasets pattern="gffcmp\.(?P<designation>.+)\.tmap" ext="tabular" /> + <filter>annotation['refmap_tmap'] != None and 'tmap' in annotation['refmap_tmap']</filter> + </collection> + </outputs> + <tests> + <!-- 2 inputs, no reference, default options --> + <test expect_num_outputs="5"> + <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> + <conditional name="annotation"> + <param name="use_ref_annotation" value="No" /> + </conditional> + <conditional name="seq_data"> + <param name="use_seq_data" value="No" /> + </conditional> + <assert_command> + <not_has_text text="-R " /> + <not_has_text text="-Q " /> + <not_has_text text="--strict-match " /> + <not_has_text text="-T " /> + <has_text_matching expression="^.*gffcompare((?!-s).)*$" /> <!-- since ln also has -s a more complicated regexp is needed here to check if -s is not set --> + <not_has_text text="-M " /> + <not_has_text text="-N " /> + <has_text text="-e 100 " /> + <has_text text="-d 100 " /> + <not_has_text text="-D " /> + <not_has_text text="--no-merge " /> + <has_text text="-p 'TCONS' " /> + <not_has_text text="-C " /> + <not_has_text text="-A " /> + <not_has_text text="-X " /> + <not_has_text text="-K " /> + </assert_command> + <output file="gffcompare_out1.stats" name="transcripts_stats" /> + <output file="gffcompare_out1.loci" name="transcripts_loci" /> + <output file="gffcompare_out1.tracking" name="transcripts_tracking" /> + <output file="gffcompare_out1.gtf" name="transcripts_combined" /> + <output_collection name="tmap_output" type="list" count="2"/> + </test> + <!-- 2 inputs, no reference, with refsequence, default options (but disable tmap output) --> + <test expect_num_outputs="4"> + <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> + <conditional name="annotation"> + <param name="use_ref_annotation" value="No" /> + <param name="refmap_tmap" value=""/> + </conditional> + <conditional name="seq_data"> + <param name="use_seq_data" value="Yes" /> + <conditional name="seq_source"> + <param name="index_source" value="history"/> + <param name="ref_file" ftype="fasta" value="sequence.fa"/> + </conditional> + </conditional> + <assert_command> + <not_has_text text="-R " /> + <not_has_text text="-Q " /> + <has_text text="-T " /> + <has_text_matching expression="gffcompare.*-s " /> <!-- since ln also has -s a more complicated regexp is needed here to check if -s is set --> + <not_has_text text="-M " /> + <not_has_text text="-N " /> + <has_text text="-e 100 " /> + <has_text text="-d 100 " /> + <has_text text="-p 'TCONS' " /> + <not_has_text text="-C " /> + <not_has_text text="-A " /> + <not_has_text text="-X " /> + <not_has_text text="-K " /> + </assert_command> + <output file="gffcompare_out1.stats" name="transcripts_stats" compare="sim_size" /> + <output file="gffcompare_out1.loci" name="transcripts_loci" compare="sim_size" /> + <output file="gffcompare_out1.tracking" name="transcripts_tracking" compare="sim_size" /> + <output file="gffcompare_out1.gtf" name="transcripts_combined" compare="sim_size" /> + </test> + <!-- 2 inputs, no reference, with cached refsequence, default options (but disable tmap output) --> + <test expect_num_outputs="4"> + <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" dbkey="hg17" /> + <conditional name="annotation"> + <param name="use_ref_annotation" value="No" /> + <param name="refmap_tmap" value=""/> + </conditional> + <conditional name="seq_data"> + <param name="use_seq_data" value="Yes" /> + <conditional name="seq_source"> + <param name="index_source" value="cached"/> + <param name="index" value="test_buildid"/> + </conditional> + </conditional> + <assert_command> + <not_has_text text="-R " /> + <not_has_text text="-Q " /> + <has_text text="-T " /> + <has_text_matching expression="gffcompare.*-s " /> + <not_has_text text="-M " /> + <not_has_text text="-N " /> + <has_text text="-e 100 " /> + <has_text text="-d 100 " /> + <has_text text="-p 'TCONS' " /> + <not_has_text text="-C " /> + <not_has_text text="-A " /> + <not_has_text text="-X " /> + <not_has_text text="-K " /> + </assert_command> + <output file="gffcompare_out1.stats" name="transcripts_stats" compare="sim_size" /> + <output file="gffcompare_out1.loci" name="transcripts_loci" compare="sim_size" /> + <output file="gffcompare_out1.tracking" name="transcripts_tracking" compare="sim_size" /> + <output file="gffcompare_out1.gtf" name="transcripts_combined" compare="sim_size" /> + </test> + <!-- 2 inputs and reference, default options --> + <test expect_num_outputs="6"> + <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> + <conditional name="annotation"> + <param name="use_ref_annotation" value="Yes" /> + <conditional name="ref_source"> + <param name="ref_source_sel" value="history"/> + <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" /> + </conditional> + </conditional> + <conditional name="seq_data"> + <param name="use_seq_data" value="No" /> + </conditional> + <assert_command> + <not_has_text text="-R " /> + <not_has_text text="-Q " /> + <not_has_text text="--strict-match " /> + <not_has_text text="-T " /> + <not_has_text text="-M " /> + <not_has_text text="-N " /> + <has_text text="-e 100 " /> + <has_text text="-d 100 " /> + <not_has_text text="-D " /> + <not_has_text text="--no-merge " /> + <not_has_text text="--chr-stats" /> + <has_text text="-p 'TCONS' " /> + <not_has_text text="-C " /> + <not_has_text text="-A " /> + <not_has_text text="-X " /> + <not_has_text text="-K " /> + </assert_command> + <output file="gffcompare_out2.stats" name="transcripts_stats" /> + <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> + <output file="gffcompare_out2.tracking" name="transcripts_tracking" /> + <output file="gffcompare_out2.gtf" name="transcripts_combined" /> + <output_collection name="refmap_output" type="list" count="2"> + <element name="gffcompare_in1_gtf" file="gffcompare_out2-1.refmap" ftype="tabular" /> + <element name="gffcompare_in2_gtf" file="gffcompare_out2-2.refmap" ftype="tabular" /> + </output_collection> + <output_collection name="tmap_output" type="list" count="2"> + <element name="gffcompare_in1_gtf" file="gffcompare_out2-1.tmap" ftype="tabular" /> + <element name="gffcompare_in2_gtf" file="gffcompare_out2-2.tmap" ftype="tabular" /> + </output_collection> + </test> + <!-- 2 inputs and reference (cached), non default options, only refmap output --> + <test expect_num_outputs="5"> + <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" dbkey="hg17" /> + <conditional name="annotation"> + <param name="use_ref_annotation" value="Yes" /> + <conditional name="ref_source"> + <param name="ref_source_sel" value="cached"/> + <param name="index" value="test_buildid"/> + </conditional> + <param name="ignore_nonoverlapping_reference" value="Yes" /> + <param name="ignore_nonoverlapping_transfrags" value="Yes" /> + <param name="strict_match" value="--strict-match" /> + <param name="refmap_tmap" value="refmap" /> + </conditional> + <conditional name="seq_data"> + <param name="use_seq_data" value="No" /> + </conditional> + <param name="discard_single_exon" value="-M"/> + <param name="discard_duplicates" value="-D"/> + <param name="no_merge" value="--no-merge" /> + <param name="max_dist_exon" value="101" /> + <param name="max_dist_group" value="99" /> + <param name="chr_stats" value="--chr-stats" /> + <assert_command> + <has_text text="-R " /> + <has_text text="-Q " /> + <has_text text="--strict-match " /> + <not_has_text text="-T " /> + <has_text text="-M " /> + <not_has_text text="-N " /> + <has_text text="-e 101 " /> + <has_text text="-d 99 " /> + <has_text text="-D " /> + <has_text text="--no-merge " /> + <has_text text="--chr-stats" /> + <has_text text="-p 'TCONS' " /> + <not_has_text text="-C " /> + <not_has_text text="-A " /> + <not_has_text text="-X " /> + <not_has_text text="-K " /> + </assert_command> + <output file="gffcompare_out2.stats" name="transcripts_stats" compare="sim_size" /> + <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> + <output file="gffcompare_out2.tracking" name="transcripts_tracking" compare="sim_size" /> + <output file="gffcompare_out2.gtf" name="transcripts_combined" compare="sim_size" delta="50000"/> + <output_collection name="refmap_output" type="list" count="0"/> <!-- because of -M no refmaps are created --> + </test> + <!-- 2 inputs and reference, non default advanced options, only tmap output --> + <test expect_num_outputs="5"> + <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> + <conditional name="annotation"> + <param name="use_ref_annotation" value="Yes" /> + <conditional name="ref_source"> + <param name="ref_source_sel" value="history"/> + <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" /> + </conditional> + <param name="refmap_tmap" value="tmap" /> + </conditional> + <conditional name="seq_data"> + <param name="use_seq_data" value="No" /> + </conditional> + <section name="adv_output"> + <param name="p" value="OTHER" /> + <param name="C" value="-C" /> + <param name="A" value="-A" /> + <param name="X" value="-X" /> + <param name="K" value="-K" /> + </section> + <assert_command> + <not_has_text text="-R " /> + <not_has_text text="-Q " /> + <not_has_text text="--strict-match " /> + <not_has_text text="-T " /> + <not_has_text text="-M " /> + <not_has_text text="-N " /> + <has_text text="-e 100 " /> + <has_text text="-d 100 " /> + <not_has_text text="-D " /> + <not_has_text text="--no-merge " /> + <not_has_text text="--chr-stats" /> + <has_text text="-p 'OTHER' " /> + <has_text text="-C " /> + <has_text text="-A " /> + <has_text text="-X " /> + <has_text text="-K " /> + </assert_command> + <output file="gffcompare_out2.stats" name="transcripts_stats" compare="sim_size" /> + <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> + <output file="gffcompare_out2.tracking" name="transcripts_tracking" compare="sim_size" /> + <output file="gffcompare_out2.gtf" name="transcripts_combined" compare="sim_size" delta="50000"/> + <output_collection name="tmap_output" type="list" count="2"/> + </test> + <!-- 2 inputs and reference, default options, no tmap or refmap output --> + <test expect_num_outputs="4"> + <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> + <conditional name="annotation"> + <param name="use_ref_annotation" value="Yes" /> + <conditional name="ref_source"> + <param name="ref_source_sel" value="history"/> + <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" /> + </conditional> + <param name="refmap_tmap" value="" /> + </conditional> + <conditional name="seq_data"> + <param name="use_seq_data" value="No" /> + </conditional> + <assert_command> + <not_has_text text="-R " /> + <not_has_text text="-Q " /> + <not_has_text text="--strict-match " /> + <has_text text="-T " /> + <not_has_text text="-M " /> + <not_has_text text="-N " /> + <has_text text="-e 100 " /> + <has_text text="-d 100 " /> + <not_has_text text="-D " /> + <not_has_text text="--no-merge " /> + <not_has_text text="--chr-stats" /> + <has_text text="-p 'TCONS' " /> + <not_has_text text="-C " /> + <not_has_text text="-A " /> + <not_has_text text="-X " /> + <not_has_text text="-K " /> + </assert_command> + <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="2" /> + <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> + <output file="gffcompare_out2.tracking" name="transcripts_tracking" /> + <output file="gffcompare_out2.gtf" name="transcripts_combined" /> + </test> + + <test expect_num_outputs="4"> + <param ftype="gtf" name="gffinputs" value="gffcompare_in4.gtf" /> + <conditional name="annotation"> + <param name="use_ref_annotation" value="Yes" /> + <conditional name="ref_source"> + <param name="ref_source_sel" value="history"/> + <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" /> + </conditional> + <param name="ignore_nonoverlapping_reference" value="Yes" /> + <param name="ignore_nonoverlapping_transfrags" value="No" /> + <param name="refmap_tmap" value="" /> + </conditional> + <param name="use_seq_data" value="No" /> + <param name="discard_single_exon" value="" /> + <param name="max_dist_exon" value="100" /> + <param name="max_dist_group" value="100" /> + <output file="gffcompare_out3.stats" name="transcripts_stats"/> + <output file="gffcompare_out3.loci" name="transcripts_loci" compare="sim_size" /> + <output file="gffcompare_out3.tracking" name="transcripts_tracking" /> + <output file="gffcompare_out3.gtf" name="transcripts_annotated" /> + </test> + </tests> + <help> +<![CDATA[ +**GffCompare Overview** + +## GffCompare +* compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie). +* collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples) +* classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a +annotation file (also in GTF/GFF3 format) + +More information can be found here: https://ccb.jhu.edu/software/stringtie/gffcompare.shtml. + +The original form of this program is also distributed as part of the Cufflinks suite, under the name "CuffCompare" +(see manual: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/). Most of the options and parameters of CuffCompare +are supported by GffCompare, while new features will likely be added to GffCompare in the future. + +A notable difference of GffCompare is that when a single query GTF/GFF file is given as input, along with a reference annotation (-r option), +gffcompare switches into "annotation mode" and it generates a .annotated.gtf file instead of the .merged.gtf produced by CuffCompare with the +same parameters. This file has the same general format as CuffCompare's .merged.gtf file (with "class codes" assigned to transcripts as per +their relationship with the matching/overlapping reference transcript), but the original transcript IDs are preserved, so gffcompare can thus +be used as a simple way of annotating a set of transcripts. + +Another important difference is that the input transcripts are no longer discarded when they are found to be "intron redundant", i.e. +contained within other, longer isoforms. CuffCompare had the -G option to prevent collapsing of such intron redundant isoforms into +their longer "containers", but GffCompare has made this the default mode of operation (hence the -G option is no longer needed +and is simply ignored when given). + ]]> + </help> + <citations> + <citation type="doi">10.1038/nbt.1621</citation> + </citations> +</tool>