Mercurial > repos > enios > nc_rna
changeset 17:308d4a7877a7 draft
Deleted selected files
| author | enios |
|---|---|
| date | Sat, 22 May 2021 07:34:38 +0000 |
| parents | 24d0a81802d6 |
| children | 11d232ed904c |
| files | gffcompare.xml |
| diffstat | 1 files changed, 0 insertions(+), 499 deletions(-) [+] |
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--- a/gffcompare.xml Sat May 22 07:30:49 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,499 +0,0 @@ -<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>