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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit cbba6947f1380751e1db3fa5b043af630523fd86 |
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modified:
repeatmasker.xml test-data/small.fasta.stats |
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added:
test-data/fake_repbase.embl test-data/small_repbase.fasta.log test-data/small_repbase.fasta.stats |
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| diff -r bdfc22c1c3e3 -r 04f5c3d7448e repeatmasker.xml --- a/repeatmasker.xml Wed May 02 20:18:11 2018 -0400 +++ b/repeatmasker.xml Fri May 04 07:59:50 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7" profile="17.01"> +<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy1" profile="17.01"> <description>RepeatMasker</description> <requirements> @@ -11,7 +11,7 @@ export REPEATMASKER_LIB_DIR=\$(pwd)/lib && for file in \$(ls \$RM_LIB_PATH) ; do ln -s \$RM_LIB_PATH/\$file lib/\$file ; done && #if $repeat_source.source_type == "repbase": - cp '${repeat_source.repbase_file}' lib/RMRBSeqs.embl && + cp '${repeat_source.repbase_file}' 'lib/${repeat_source.repbase_file_name}' && #end if ln -s '${input_fasta}' rm_input.fasta && RepeatMasker -dir \$(pwd) @@ -26,31 +26,31 @@ #end if #end if -parallel \${GALAXY_SLOTS:-1} - '${gff}' - '${ignore_n_stretches}' - '${advanced.is_only}' - '${advanced.is_clip}' - '${advanced.no_is}' - '${advanced.rodspec}' - '${advanced.primspec}' - '${advanced.nolow}' - '${advanced.noint}' - '${advanced.norna}' - '${advanced.alu}' - '${advanced.div}' - '${advanced.search_speed}' - '${advanced.frag}' - '${advanced.maxsize}' - #if $advanced.gc is not None: - '${advanced.gc}' + ${gff} + ${excln} + ${advanced.is_only} + ${advanced.is_clip} + ${advanced.no_is} + ${advanced.rodspec} + ${advanced.primspec} + ${advanced.nolow} + ${advanced.noint} + ${advanced.norna} + ${advanced.alu} + ${advanced.div} + ${advanced.search_speed} + -frag ${advanced.frag} + ## -maxsize ${advanced.maxsize} + #if str($advanced.gc): + -gc ${advanced.gc} #end if - '${advanced.gccalc}' - '${advanced.nocut}' - '${advanced.keep_alignments}' - '${advanced.invert_alignments}' - '${advanced.xout}' - '${advanced.xsmall}' - '${advanced.poly}' + ${advanced.gccalc} + ${advanced.nocut} + ${advanced.keep_alignments} + ${advanced.invert_alignments} + ${advanced.xout} + ${advanced.xsmall} + ${advanced.poly} rm_input.fasta && #if $advanced.is_only != '-is_only': mv rm_input.fasta.masked '${output_masked_genome}' && @@ -79,6 +79,7 @@ </param> <when value="repbase"> <param name="repbase_file" type="data" format="embl" label="RepBase (RMRBSeqs.embl) file" /> + <param name="repbase_file_name" type="hidden" value="RMRBSeqs.embl"/> <!-- This is an ugly hack to allow testing with a fake repbase --> <conditional name="species_source"> <param label="Select species name from a list?" name="species_from_list" type="select"> <option value="yes" selected="true">Yes</option> @@ -126,7 +127,7 @@ </when> </conditional> <param type="boolean" argument="-gff" truevalue="-gff" falsevalue="" label="Output annotation of repeats in GFF format" checked="false" /> - <param name="ignore_n_stretches" type="boolean" argument="-excln" falsevalue="" label="Ignore stretches of Ns when computing statistics" checked="true" help="Scaffolds are sometimes joined with stretches of 25 or more Ns. This option ignores them when calculating repeat statistics" /> + <param argument="-excln" type="boolean" truevalue="-excln" falsevalue="" label="Ignore stretches of Ns when computing statistics" checked="true" help="Scaffolds are sometimes joined with stretches of 25 or more Ns. This option ignores them when calculating repeat statistics" /> <section name="advanced" title="Advanced options" expanded="false"> <param argument="-is_only" type="boolean" truevalue="-is_only" falsevalue="" checked="false" label="Only clip E coli insertion elements" /> <param argument="-is_clip" type="boolean" truevalue="-is_clip" falsevalue="" checked="false" label="Clip IS elements before analysis" help="Normally RepeatMasker will report on IS element, with this option selected it will clip them before analysis" /> @@ -145,8 +146,9 @@ <option value="-s">Slow (0-5% more sensitive, 2.5 times slowdown)</option> </param> <param type="integer" argument="-frag" value="40000" label="Maximum contiguous sequence searched" help="Maximum length of sequencing that is search without fragmenting" /> - <param type="integer" argument="-maxsize" value="4000000" label="Maximum length for IS or repeat clipped sequences" /> - <param type="integer" argument="-gc" optional="True" label="Select matrices for this GC%" help="Valid values are a percentage or -1 to choose the default" /> + <!-- -maxsize option is in the help, but not in the code of repeatmasker--> + <!--param type="integer" argument="-maxsize" value="4000000" label="Maximum length for IS or repeat clipped sequences" /--> + <param type="integer" argument="-gc" optional="true" label="Select matrices for this GC%" help="Valid values are a percentage or -1 to choose the default" /> <param type="boolean" argument="-gccalc" truevalue="-gcccalc" falsevalue="" checked="false" label="Calculate GC % for all sequences" help="By default RepeatMasker skips calculating GC % for small sequences" /> <param type="boolean" argument="-nocut" truevalue="-nocut" falsevalue="" checked="false" label="Skips cutting of repeats" /> <param name="xout" type="boolean" argument="-x" truevalue="-x" falsevalue="" checked="false" label="Mask with X instead of N characters" /> @@ -203,6 +205,17 @@ <output name="output_polymorphic" file="small.fasta.poly" /> <output name="output_gff" file="small.fasta.gff" lines_diff="4" /> </test> + <test expect_num_outputs="4"> + <param name="input_fasta" value="small.fasta" ftype="fasta" /> + <param name="source_type" value="repbase" /> + <param name="repbase_file" value="fake_repbase.embl" /> + <param name="repbase_file_name" value="fake.embl" /> + <param name="species_list" value="anopheles" /> + <output name="output_masked_genome" file="small.fasta.masked" /> + <output name="output_table" file="small_repbase.fasta.stats" lines_diff="2" /> + <output name="output_repeat_catalog" file="small.fasta.cat" /> + <output name="output_log" file="small_repbase.fasta.log" /> + </test> </tests> <help><![CDATA[ RepeatMasker is a program that screens DNA for interspersed repeats and low |
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| diff -r bdfc22c1c3e3 -r 04f5c3d7448e test-data/fake_repbase.embl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fake_repbase.embl Fri May 04 07:59:50 2018 -0400 |
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| @@ -0,0 +1,21 @@ +CC Fake repbase-like embl file, using data from DfamConsensus.embl* +CC **************************************************************** +XX +ID ACROBAT1 repeatmasker; DNA; ???; 768 BP. +CC consensus - See RepBase for additional annotations. +XX +SQ Sequence 768 BP; 178 A; 194 C; 215 G; 181 T; 0 other; + ggtgatgctg ccaacttact gatttagtgt atgatggtgt ttttgaggtg ctccagtggc 60 + ttctgtttct atcagctgtc cctcctgttc agctactgac ggggtggtgc gtaacggcaa 120 + aagcaccgcc ggacatcagc gctatctctg ctctcactgc cgtaaaacat ggcaactgca 180 + gttcacttac accgcttctc aacccggtac gcaccagaaa atcattgata tggccatgaa 240 + tggcgttgga tgccgggcaa cagcccgcat tatgggcgtt ggcctcaaca cgattttacg 300 + tcacttaaaa aactcaggcc gcagtcggta acctcgcgca tacagccggg cagtgacgtc 360 + atcgtctgcg cggaaatgga cgaacagtgg ggctatgtcg gggctaaatc gcgccagcgc 420 + tggctgtttt acgcgtatga cagtctccgg aagacggttg ttgcgcacgt attcggtgaa 480 + cgcactatgg cgacgctggg gcgtcttatg agcctgctgt caccctttga cgtggtgata 540 + tggatgacgg atggctggcc gctgtatgaa tcccgcctga agggaaagct gcacgtaatc 600 + agcaagcgat atacgcagcg aattgagcgg cataacctga atctgaggca gcacctggca 660 + cggctgggac ggaagtcgct gtcgttctca aaatcggtgg agctgcatga caaagtcatc 720 + gggcattatc tgaacataaa acactatcaa taagttggag tcattacc 768 +// |
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| diff -r bdfc22c1c3e3 -r 04f5c3d7448e test-data/small.fasta.stats --- a/test-data/small.fasta.stats Wed May 02 20:18:11 2018 -0400 +++ b/test-data/small.fasta.stats Fri May 04 07:59:50 2018 -0400 |
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| @@ -41,7 +41,8 @@ * most repeats fragmented by insertions or deletions have been counted as one element - + Runs of >=20 X/Ns in query were excluded in % calcs + The query species was assumed to be homo RepeatMasker Combined Database: Dfam_Consensus-20170127 |
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| diff -r bdfc22c1c3e3 -r 04f5c3d7448e test-data/small_repbase.fasta.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_repbase.fasta.log Fri May 04 07:59:50 2018 -0400 |
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| @@ -0,0 +1,10 @@ +SW score % div. % del. % ins. query sequence pos in query: begin end (left) repeat class/family pos in repeat: begin end (left) ID + +18 0.0 0.0 0.0 scaffold_1 613 632 (13588) (GT)n Simple_repeat 1 20 (0) 1 +16 18.3 2.2 2.2 scaffold_1 780 824 (13396) (ATAATA)n Simple_repeat 1 45 (0) 2 +12 23.9 4.5 0.0 scaffold_1 2231 2274 (11946) (CAGA)n Simple_repeat 1 46 (0) 3 +15 18.4 10.2 0.0 scaffold_1 4853 4901 (9319) (TC)n Simple_repeat 1 54 (0) 4 +13 19.1 1.8 7.7 scaffold_1 6230 6284 (7936) (TAATTAA)n Simple_repeat 1 52 (0) 5 +15 28.3 0.0 3.5 scaffold_1 6548 6606 (7614) (GACA)n Simple_repeat 1 57 (0) 6 +67 2.9 1.4 0.0 scaffold_1 11981 12050 (2170) (CT)n Simple_repeat 1 71 (0) 7 +19 15.4 2.8 0.0 scaffold_1 12078 12113 (2107) (CT)n Simple_repeat 1 37 (0) 7 |
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| diff -r bdfc22c1c3e3 -r 04f5c3d7448e test-data/small_repbase.fasta.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_repbase.fasta.stats Fri May 04 07:59:50 2018 -0400 |
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| @@ -0,0 +1,60 @@ +================================================== +file name: rm_input.fasta +sequences: 1 +total length: 14220 bp (14220 bp excl N/X-runs) +GC level: 39.94 % +bases masked: 378 bp ( 2.66 %) +================================================== + number of length percentage + elements* occupied of sequence +-------------------------------------------------- +Retroelements 0 0 bp 0.00 % + SINEs: 0 0 bp 0.00 % + Penelope 0 0 bp 0.00 % + LINEs: 0 0 bp 0.00 % + CRE/SLACS 0 0 bp 0.00 % + L2/CR1/Rex 0 0 bp 0.00 % + R1/LOA/Jockey 0 0 bp 0.00 % + R2/R4/NeSL 0 0 bp 0.00 % + RTE/Bov-B 0 0 bp 0.00 % + L1/CIN4 0 0 bp 0.00 % + LTR elements: 0 0 bp 0.00 % + BEL/Pao 0 0 bp 0.00 % + Ty1/Copia 0 0 bp 0.00 % + Gypsy/DIRS1 0 0 bp 0.00 % + Retroviral 0 0 bp 0.00 % + +DNA transposons 0 0 bp 0.00 % + hobo-Activator 0 0 bp 0.00 % + Tc1-IS630-Pogo 0 0 bp 0.00 % + En-Spm 0 0 bp 0.00 % + MuDR-IS905 0 0 bp 0.00 % + PiggyBac 0 0 bp 0.00 % + Tourist/Harbinger 0 0 bp 0.00 % + Other (Mirage, 0 0 bp 0.00 % + P-element, Transib) + +Rolling-circles 0 0 bp 0.00 % + +Unclassified: 0 0 bp 0.00 % + +Total interspersed repeats: 0 bp 0.00 % + + +Small RNA: 0 0 bp 0.00 % + +Satellites: 0 0 bp 0.00 % +Simple repeats: 7 378 bp 2.66 % +Low complexity: 0 0 bp 0.00 % +================================================== + +* most repeats fragmented by insertions or deletions + have been counted as one element + Runs of >=20 X/Ns in query were excluded in % calcs + + +The query species was assumed to be anopheles genus +RepeatMasker Combined Database: Dfam_Consensus-20170127 + +run with rmblastn version 2.2.27+ + |