| Previous changeset 3:2bb86e2c417f (2019-05-27) Next changeset 5:f99dd58de04f (2023-02-03) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5" |
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modified:
gffcompare.xml test-data/gffcompare_out3.stats |
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| diff -r 2bb86e2c417f -r 0f710191a66d gffcompare.xml --- a/gffcompare.xml Mon May 27 13:54:15 2019 -0400 +++ b/gffcompare.xml Thu Oct 17 03:01:26 2019 -0400 |
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| b'@@ -3,7 +3,7 @@\n <macros>\n <token name="@GFFCOMPARE_VERSION@">0.11.2</token>\n </macros>\n-\t<requirements>\n+ <requirements>\n <requirement type="package" version="@GFFCOMPARE_VERSION@">gffcompare</requirement>\n </requirements>\n <version_command>gffcompare -v | awk \'{print $2}\'</version_command>\n@@ -49,6 +49,7 @@\n \n $discard_single_exon\n $discard_duplicates\n+$no_merge\n -e $max_dist_exon\n -d $max_dist_group\n $chr_stats\n@@ -79,7 +80,7 @@\n <when value="cached">\n <param argument="-r" label="Using reference annotation" name="index" type="select">\n <options from_data_table="gene_sets">\n- <filter column="1" key="dbkey" ref="gffinputs" type="data_meta" />\n+ <filter column="dbkey" key="dbkey" ref="gffinputs" type="data_meta" />\n </options>\n <validator message="No reference annotation is available for the build associated with the selected input dataset" type="no_options" />\n </param>\n@@ -117,7 +118,7 @@\n <when value="cached">\n <param argument="-s" label="Using reference genome" name="index" type="select">\n <options from_data_table="fasta_indexes">\n- <filter column="1" key="dbkey" ref="gffinputs" type="data_meta" />\n+ <filter column="dbkey" key="dbkey" ref="gffinputs" type="data_meta" />\n </options>\n <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />\n </param>\n@@ -143,7 +144,7 @@\n <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" />\n <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" />\n <section name="adv_output" title="Options for the combined GTF output file">\n- <param argument="-p" type="text" value="TCONS" label="name prefix for consensus transcripts" help="for combined.gtf (default: \'TCONS\')" />\n+ <param argument="-p" type="text" value="TCONS" label="name prefix for consensus transcripts" help="for combined.gtf" />\n <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" />\n <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" />\n <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" />\n@@ -184,14 +185,14 @@\n <not_has_text text="-Q " />\n <not_has_text text="--strict-match " />\n <not_has_text text="-T " />\n- <not_has_text text="-s " />\n+ <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 -->\n <not_has_text text="-M " />\n <not_has_text text="-N " />\n <has_te'..b' <not_has_text text="-K " />\n </assert_command>\n- <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" />\n- <output file="gffcompare_out2.loci" name="transcripts_loci" lines_diff="2" />\n+ <output file="gffcompare_out2.stats" name="transcripts_stats" />\n+ <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" />\n <output file="gffcompare_out2.tracking" name="transcripts_tracking" />\n <output file="gffcompare_out2.gtf" name="transcripts_combined" />\n <output_collection name="refmap_output" type="list" count="2">\n@@ -346,7 +351,7 @@\n <has_text text="-D " />\n <has_text text="--no-merge " />\n <has_text text="--chr-stats" />\n- <not_has_text text="-p TCONS " />\n+ <has_text text="-p \'TCONS\' " />\n <not_has_text text="-C " />\n <not_has_text text="-A " />\n <not_has_text text="-X " />\n@@ -382,12 +387,16 @@\n <assert_command>\n <not_has_text text="-R " />\n <not_has_text text="-Q " />\n+ <not_has_text text="--strict-match " />\n <not_has_text text="-T " />\n <not_has_text text="-M " />\n <not_has_text text="-N " />\n <has_text text="-e 100 " />\n <has_text text="-d 100 " />\n- <has_text text="-p OTHER " />\n+ <not_has_text text="-D " />\n+ <not_has_text text="--no-merge " />\n+ <not_has_text text="--chr-stats" />\n+ <has_text text="-p \'OTHER\' " />\n <has_text text="-C " />\n <has_text text="-A " />\n <has_text text="-X " />\n@@ -416,19 +425,23 @@\n <assert_command>\n <not_has_text text="-R " />\n <not_has_text text="-Q " />\n+ <not_has_text text="--strict-match " />\n <has_text text="-T " />\n <not_has_text text="-M " />\n <not_has_text text="-N " />\n <has_text text="-e 100 " />\n <has_text text="-d 100 " />\n- <has_text text="-p TCONS " />\n+ <not_has_text text="-D " />\n+ <not_has_text text="--no-merge " />\n+ <not_has_text text="--chr-stats" />\n+ <has_text text="-p \'TCONS\' " />\n <not_has_text text="-C " />\n <not_has_text text="-A " />\n <not_has_text text="-X " />\n <not_has_text text="-K " />\n </assert_command>\n- <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" />\n- <output file="gffcompare_out2.loci" name="transcripts_loci" lines_diff="2" />\n+ <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="2" />\n+ <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" />\n <output file="gffcompare_out2.tracking" name="transcripts_tracking" />\n <output file="gffcompare_out2.gtf" name="transcripts_combined" />\n </test>\n@@ -449,8 +462,8 @@\n <param name="discard_single_exon" value="" />\n <param name="max_dist_exon" value="100" />\n <param name="max_dist_group" value="100" />\n- <output file="gffcompare_out3.stats" name="transcripts_stats" lines_diff="6" />\n- <output file="gffcompare_out3.loci" name="transcripts_loci" />\n+ <output file="gffcompare_out3.stats" name="transcripts_stats"/>\n+ <output file="gffcompare_out3.loci" name="transcripts_loci" compare="sim_size" />\n <output file="gffcompare_out3.tracking" name="transcripts_tracking" />\n <output file="gffcompare_out3.gtf" name="transcripts_annotated" />\n </test>\n' |
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| diff -r 2bb86e2c417f -r 0f710191a66d test-data/gffcompare_out3.stats --- a/test-data/gffcompare_out3.stats Mon May 27 13:54:15 2019 -0400 +++ b/test-data/gffcompare_out3.stats Thu Oct 17 03:01:26 2019 -0400 |
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| @@ -1,29 +1,29 @@ -# gffcompare v0.10.6 | Command line was: +# gffcompare v0.11.2 | Command line was: #gffcompare -r ref_annotation -R -T -e 100 -d 100 -p TCONS gffcompare_in4_gtf # #= Summary for dataset: gffcompare_in4_gtf # Query mRNAs : 35 in 29 loci (15 multi-exon transcripts) # (3 multi-transcript loci, ~1.2 transcripts per locus) -# Reference mRNAs : 20 in 7 loci (19 multi-exon) +# Reference mRNAs : 19 in 6 loci (19 multi-exon) # Super-loci w/ reference transcripts: 6 #-----------------| Sensitivity | Precision | - Base level: 72.6 | 60.7 | - Exon level: 80.0 | 55.7 | + Base level: 72.7 | 60.7 | + Exon level: 81.0 | 55.7 | Intron level: 81.2 | 64.4 | Intron chain level: 10.5 | 13.3 | - Transcript level: 10.0 | 5.7 | - Locus level: 28.6 | 6.9 | + Transcript level: 10.5 | 5.7 | + Locus level: 33.3 | 6.9 | Matching intron chains: 2 Matching transcripts: 2 Matching loci: 2 - Missed exons: 3/85 ( 3.5%) + Missed exons: 2/84 ( 2.4%) Novel exons: 46/122 ( 37.7%) Missed introns: 11/69 ( 15.9%) Novel introns: 28/87 ( 32.2%) - Missed loci: 0/7 ( 0.0%) + Missed loci: 0/6 ( 0.0%) Novel loci: 15/29 ( 51.7%) Total union super-loci across all input datasets: 21 |