| Previous changeset 8:ade773848c3d (2020-01-23) Next changeset 10:bfc70c8cc5ca (2020-12-11) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 7f117678cfee55bb18706fd1bf14c0a380261eab" |
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modified:
repeatmasker.xml test-data/small.fasta.cat test-data/small.fasta.gff test-data/small.fasta.stats test-data/small_repbase.fasta.stats |
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| diff -r ade773848c3d -r 438f65cb1d14 repeatmasker.xml --- a/repeatmasker.xml Thu Jan 23 04:40:29 2020 -0500 +++ b/repeatmasker.xml Tue Aug 18 05:39:55 2020 -0400 |
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| @@ -1,12 +1,12 @@ -<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy2" profile="17.01"> +<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.9" profile="17.01"> <description>screen DNA sequences for interspersed repeats and low complexity regions</description> <requirements> - <requirement type="package" version="4.0.7">repeatmasker</requirement> + <requirement type="package" version="4.0.9_p2">repeatmasker</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - RM_PATH=\$(which RepeatMasker) && + RM_PATH=\$(which RepeatMasker) && if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi && RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries && mkdir lib && |
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| diff -r ade773848c3d -r 438f65cb1d14 test-data/small.fasta.cat --- a/test-data/small.fasta.cat Thu Jan 23 04:40:29 2020 -0500 +++ b/test-data/small.fasta.cat Tue Aug 18 05:39:55 2020 -0400 |
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| @@ -98,6 +98,6 @@ ## Total Length: 14220 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 ## Total NonSub ( excluding all non ACGT bases ):14220 -RepeatMasker version open-4.0.7 , default mode -run with rmblastn version 2.2.27+ -RepeatMasker Combined Database: Dfam_Consensus-20170127 +RepeatMasker version open-4.0.9 , default mode +run with rmblastn version 2.9.0+ +RepeatMasker Combined Database: Dfam-Dfam_3.0 |
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| diff -r ade773848c3d -r 438f65cb1d14 test-data/small.fasta.gff --- a/test-data/small.fasta.gff Thu Jan 23 04:40:29 2020 -0500 +++ b/test-data/small.fasta.gff Tue Aug 18 05:39:55 2020 -0400 |
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| @@ -1,6 +1,6 @@ ##gff-version 2 -##date 2018-04-21 -##sequence-region dataset_12.dat +##date 2020-08-18 +##sequence-region rm_input.fasta scaffold_1 RepeatMasker similarity 613 632 0.0 + . Target "Motif:(GT)n" 1 20 scaffold_1 RepeatMasker similarity 780 824 18.3 + . Target "Motif:(ATAATA)n" 1 45 scaffold_1 RepeatMasker similarity 2231 2274 23.9 + . Target "Motif:(CAGA)n" 1 46 |
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| diff -r ade773848c3d -r 438f65cb1d14 test-data/small.fasta.stats --- a/test-data/small.fasta.stats Thu Jan 23 04:40:29 2020 -0500 +++ b/test-data/small.fasta.stats Tue Aug 18 05:39:55 2020 -0400 |
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| @@ -1,5 +1,5 @@ ================================================== -file name: dataset_12.dat +file name: rm_input.fasta sequences: 1 total length: 14220 bp (14220 bp excl N/X-runs) GC level: 39.94 % @@ -45,8 +45,8 @@ The query species was assumed to be homo -RepeatMasker Combined Database: Dfam_Consensus-20170127 - -run with rmblastn version 2.2.27+ -The query was compared to unclassified sequences in ".../dataset_2.dat" +RepeatMasker Combined Database: Dfam-Dfam_3.0 + +run with rmblastn version 2.9.0+ +The query was compared to unclassified sequences in ".../dataset_257a7a8f-7065-486a-ae21-53e1fceff0f8.dat" |
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| diff -r ade773848c3d -r 438f65cb1d14 test-data/small_repbase.fasta.stats --- a/test-data/small_repbase.fasta.stats Thu Jan 23 04:40:29 2020 -0500 +++ b/test-data/small_repbase.fasta.stats Tue Aug 18 05:39:55 2020 -0400 |
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| @@ -54,7 +54,7 @@ The query species was assumed to be anopheles genus -RepeatMasker Combined Database: Dfam_Consensus-20170127 - -run with rmblastn version 2.2.27+ +RepeatMasker Combined Database: Dfam-Dfam_3.0 + +run with rmblastn version 2.9.0+ |