| Previous changeset 3:3de2195f32c0 (2020-11-13) Next changeset 5:f5a5a2b39ff2 (2021-03-25) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" |
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modified:
lastal.xml lastdb.xml lastsplit.xml lasttrain.xml macros_last.xml maf-convert.xml test-data/last_align_fastq.maf test-data/last_align_gen.maf test-data/last_align_prot.maf test-data/last_split.maf test-data/last_train.txt test-data/last_train_E.txt |
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added:
test-data/fuguMito.fa.gz test-data/fuguMito.fq.gz test-data/humanMito.fa.gz test-data/humanMito.fq.gz |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f lastal.xml --- a/lastal.xml Fri Nov 13 09:05:49 2020 +0000 +++ b/lastal.xml Wed Mar 24 22:36:50 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="last_al" name="LASTal" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01"> +<tool id="last_al" name="LASTal" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01"> <description>finds local alignments between query sequences, and reference sequences.</description> @@ -11,21 +11,28 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ + set -e -o pipefail; + #if $db_opts.db_opts_input == 'lastdb' ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' && #end if - - lastal - #if $query_seq.ext == 'fasta' + #if $query_seq.ext.endswith('.gz') + zcat + #else + cat + #end if + '$query_seq' | lastal + + #if $query_seq.ext.startswith('fasta') -Q 0 - #else if $query_seq.ext == 'fastqsanger' + #else if $query_seq.ext.startswith('fastqsanger') -Q 1 - #else if $query_seq.ext == 'fastqsolexa' + #else if $query_seq.ext.startswith('fastqsolexa') -Q 2 - #else if $query_seq.ext == 'fastqillumina' + #else if $query_seq.ext.startswith('fastqillumina') -Q 3 - #else if $query_seq.ext == 'pssm' + #else if $query_seq.ext.startswith('pssm') -Q 5 #end if @@ -79,14 +86,12 @@ 'db_files/lastdb' #end if - '$query_seq' - >'$outfile' ]]></command> <inputs> <expand macro="input_db"/> - <param name="query_seq" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina,tabular" label="Query sequences"/> + <param name="query_seq" type="data" format="fasta,fasta.gz,fastq,fastq.gz,tabular" label="Query sequences"/> <section name="lastal" title="Lastal arguments" expanded="true"> <param argument="-f" type="select" multiple="false" label="Output format"> @@ -348,7 +353,7 @@ <param name="db_opts_input" value="db"/> <param name="database" value="humdb"/> </conditional> - <param name="query_seq" value="fuguMito.fa" ftype="fasta"/> + <param name="query_seq" value="fuguMito.fa.gz" ftype="fasta.gz"/> <output name="outfile" ftype="maf" file="last_align_gen.maf" lines_diff="2"/> </test> <test> @@ -369,7 +374,7 @@ <param name="db_opts_input" value="db"/> <param name="database" value="humdb-sanger"/> </conditional> - <param name="query_seq" value="fuguMito.fq" ftype="fastqsanger"/> + <param name="query_seq" value="fuguMito.fq.gz" ftype="fastqsanger.gz"/> <section name="lastal"> <param name="Q" value="1"/> </section> |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f lastdb.xml --- a/lastdb.xml Fri Nov 13 09:05:49 2020 +0000 +++ b/lastdb.xml Wed Mar 24 22:36:50 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="last_db" name="LASTdb" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01"> +<tool id="last_db" name="LASTdb" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01"> <description>prepares sequences for subsequent comparison and alignment using lastal.</description> @@ -11,15 +11,22 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ - lastdb + set -e -o pipefail; - #if $input_files.ext == 'fasta' + #if $input_files.ext.endswith('.gz') + zcat + #else + cat + #end if + '$input_files' | lastdb + + #if $input_files.ext.startswith('fasta') -Q 0 - #else if $input_files.ext == 'fastqsanger' + #else if $input_files.ext.startswith('fastqsanger') -Q 1 - #else if $input_files.ext == 'fastqsolexa' + #else if $input_files.ext.startswith('fastqsolexa') -Q 2 - #else if $input_files.ext == 'fastqillumina' + #else if $input_files.ext.startswith('fastqillumina') -Q 3 #end if $lastdb.sequences_type.protein @@ -29,14 +36,16 @@ -S $lastdb.lastdb_advanced.S -u $lastdb.lastdb_advanced.seeds.u -w $lastdb.lastdb_advanced.seeds.w - -W $lastdb.lastdb_advanced.seeds.W + #if $lastdb.lastdb_advanced.seeds.W + -W $lastdb.lastdb_advanced.seeds.W + #end if -m $lastdb.lastdb_advanced.seeds.m -i $lastdb.lastdb_advanced.i -C $lastdb.lastdb_advanced.C -s \${GALAXY_MEMORY_MB:-2G} -P \${GALAXY_SLOTS:-1} 'lastdb' - '$input_files' + && @@ -45,7 +54,7 @@ ]]></command> <inputs> - <param name="input_files" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina" label="Reference(s) input files" /> + <param name="input_files" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Reference(s) input files" /> <section name="lastdb" title="Lastdb arguments" expanded="true"> <conditional name="sequences_type"> <param name="protein" type="select" multiple="false" label="The sequences are :"> @@ -81,7 +90,7 @@ </param> <conditional name="seeds"> - <param argument="-u" type="select" multiple="false" label="Specify a seeding scheme."> + <param argument="-u" type="select" multiple="false" optional="true" label="Specify a seeding scheme."> <option value="BISF">BISF</option> <option value="BISR">BISR</option> <option value="MAM4">MAM4</option> @@ -134,7 +143,7 @@ <tests> <test> - <param name="input_files" value="humanMito.fa" ftype="fasta"/> + <param name="input_files" value="humanMito.fa.gz" ftype="fasta.gz"/> <section name="lastdb"> <section name="repeats"> <param name="uppercase" value="0"/> @@ -145,7 +154,7 @@ <output name="outfile" compare="contains" file="humdb.lastdb" ftype="lastdb"> <extra_files type="file" value="humdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/> <extra_files type="file" value="humdb.des" name="lastdb.des"/> - <extra_files type="file" value="humdb.prj" name="lastdb.prj"/> + <extra_files type="file" value="humdb.prj" name="lastdb.prj" compare="sim_size" delta="2"/> <extra_files type="file" value="humdb.sds" name="lastdb.sds"/> <extra_files type="file" value="humdb.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/> <extra_files type="file" value="humdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/> @@ -159,6 +168,10 @@ <param name="protein" value="-p"/> </conditional> </section> + <section name="lastdb_advanced"> + <conditional name="seeds"> + <param name="u" value="MURPHY10"/> + </section> <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb"> <extra_files type="file" value="hedgdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/> <extra_files type="file" value="hedgdb.des" name="lastdb.des"/> @@ -170,7 +183,7 @@ </output> </test> <test> - <param name="input_files" value="humanMito.fq" ftype="fastqsanger"/> + <param name="input_files" value="humanMito.fq.gz" ftype="fastqsanger.gz"/> <section name="lastdb"> <param name="Q" value="1"/> <section name="repeats"> @@ -182,7 +195,7 @@ <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb"> <extra_files type="file" value="humdb-sanger.bck" name="lastdb.bck" compare="sim_size" delta="1"/> <extra_files type="file" value="humdb-sanger.des" name="lastdb.des"/> - <extra_files type="file" value="humdb-sanger.prj" name="lastdb.prj" lines_diff="1"/> + <extra_files type="file" value="humdb-sanger.prj" name="lastdb.prj" lines_diff="2"/> <extra_files type="file" value="humdb-sanger.sds" name="lastdb.sds"/> <extra_files type="file" value="humdb-sanger.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/> <extra_files type="file" value="humdb-sanger.suf" name="lastdb.suf" compare="sim_size" delta="1"/> |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f lastsplit.xml --- a/lastsplit.xml Fri Nov 13 09:05:49 2020 +0000 +++ b/lastsplit.xml Wed Mar 24 22:36:50 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="last_split" name="LAST-split" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01"> +<tool id="last_split" name="LAST-split" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01"> <description>finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA).</description> @@ -72,7 +72,7 @@ <param name="database" value="humdb"/> </conditional> <param name="last_align" ftype="maf" value="last_align_gen.maf"/> - <output name="outfile" ftype="maf" file="last_split.maf"/> + <output name="outfile" ftype="maf" file="last_split.maf" lines_diff="2"/> </test> </tests> |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f lasttrain.xml --- a/lasttrain.xml Fri Nov 13 09:05:49 2020 +0000 +++ b/lasttrain.xml Wed Mar 24 22:36:50 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy2" profile="18.01"> +<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01"> <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description> @@ -11,11 +11,16 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ + set -e -o pipefail; #if $db_opts.db_opts_input == 'lastdb' ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' && #end if - - last-train + #if $query_fasta.ext.endswith('.gz') + zcat + #else + cat + #end if + '$query_fasta' | last-train -Q $init_options.Q -r $init_options.r @@ -43,15 +48,13 @@ 'db_files/lastdb' #end if - '$query_fasta' - >'$outfile' ]]></command> <inputs> <expand macro="input_db" /> - <param name="query_fasta" type="data" format="fasta,fastqsanger" label="Queries input files" /> + <param name="query_fasta" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Queries input files" /> <conditional name="init_options"> <param argument="-Q" type="select" multiple="false" label="Query input format"> <option value="0" selected="true">FASTA</option> @@ -115,15 +118,15 @@ <param name="E" value="10"/> </section> </section> - <param name="query_fasta" value="fuguMito.fa"/> - <output name="outfile" file="last_train_E.txt" ftype="txt" lines_diff="22"/> + <param name="query_fasta" value="fuguMito.fa.gz" ftype="fasta.gz"/> + <output name="outfile" file="last_train_E.txt" ftype="txt" lines_diff="28"/> </test> <test> <conditional name="db_opts"> <param name="db_opts_input" value="db"/> <param name="database" value="humdb"/> </conditional> - <param name="query_fasta" value="fuguMito.fa"/> + <param name="query_fasta" value="fuguMito.fq.gz" ftype="fastqsanger.gz"/> <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/> </test> </tests> |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f macros_last.xml --- a/macros_last.xml Fri Nov 13 09:05:49 2020 +0000 +++ b/macros_last.xml Wed Mar 24 22:36:50 2021 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@LAST_CONDA_VERSION@">1021</token> + <token name="@LAST_CONDA_VERSION@">1205</token> <token name="@LAST_HELP@"><![CDATA[ Documentation : http://last.cbrc.jp/ |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f maf-convert.xml --- a/maf-convert.xml Fri Nov 13 09:05:49 2020 +0000 +++ b/maf-convert.xml Wed Mar 24 22:36:50 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="last_maf_convert" name="MAF-convert" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01"> +<tool id="last_maf_convert" name="MAF-convert" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01"> <description>read MAF-format alignments and write them in another format.</description> |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/fuguMito.fa.gz |
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| Binary file test-data/fuguMito.fa.gz has changed |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/fuguMito.fq.gz |
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| Binary file test-data/fuguMito.fq.gz has changed |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/humanMito.fa.gz |
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| Binary file test-data/humanMito.fa.gz has changed |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/humanMito.fq.gz |
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| Binary file test-data/humanMito.fq.gz has changed |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/last_align_fastq.maf --- a/test-data/last_align_fastq.maf Fri Nov 13 09:05:49 2020 +0000 +++ b/test-data/last_align_fastq.maf Wed Mar 24 22:36:50 2021 +0000 |
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| @@ -1,8 +1,8 @@ -# LAST version 1021 +# LAST version 1205 # # a=7 b=1 A=7 B=1 e=22 d=13 x=21 y=9 z=21 D=1e+06 # R=10 u=0 s=2 S=0 M=0 T=0 m=10 l=1 L=999999999 n=10 k=1 w=1000 t=2.82533 j=3 Q=1 -# db_files/lastdb +# /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb-sanger # Reference sequences=1 normal letters=16571 # # A R N D C Q E G H I L K M F P S T W Y V B J Z X * |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/last_align_gen.maf --- a/test-data/last_align_gen.maf Fri Nov 13 09:05:49 2020 +0000 +++ b/test-data/last_align_gen.maf Wed Mar 24 22:36:50 2021 +0000 |
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| @@ -1,8 +1,8 @@ -# LAST version 1021 +# LAST version 1205 # # a=7 b=1 A=7 B=1 e=22 d=13 x=21 y=9 z=21 D=1e+06 # R=10 u=0 s=2 S=0 M=0 T=0 m=10 l=1 L=999999999 n=10 k=1 w=1000 t=2.82533 j=3 Q=0 -# ref_db +# /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb # Reference sequences=1 normal letters=16571 # # A R N D C Q E G H I L K M F P S T W Y V B J Z X * |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/last_align_prot.maf --- a/test-data/last_align_prot.maf Fri Nov 13 09:05:49 2020 +0000 +++ b/test-data/last_align_prot.maf Wed Mar 24 22:36:50 2021 +0000 |
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| @@ -1,8 +1,8 @@ -# LAST version 1021 +# LAST version 1205 # # a=11 b=2 A=11 B=2 e=22 d=13 x=21 y=9 z=21 D=1e+06 E=2.73494e+09 # R=10 u=0 s=1 S=0 M=0 T=0 m=10 l=1 L=999999999 n=10 k=1 w=1000 t=3.08611 j=3 Q=0 -# ref_db +# /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/hedgdb # Reference sequences=1 normal letters=411 # lambda=0.305935 K=0.102404 # @@ -39,28 +39,4 @@ # name start alnSize strand seqSize alignment # # batch 0 -a score=729 EG2=1.4e-80 E=1.2e-101 -s NP_002172.2 13 264 + 411 LVLLLLLVVPA----AWGCGPGRVVGSRRRPPRKLVPLAYKQFSPNVPEKTLGASGRYEGKIARSSERFKELTPNYNPDIIFKDEENTGADRLMTQRCKDRLNSLAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYGLLARLAVEAGFDWVYYESKAHVHCSVKSEHSAAAKTGGCFPAGAQVRLESGARVALSAVRPGDRVLAMGEDGSPTFSDVLIFLDREPHRLRAFQVIETQDPPRRLALTPAHLL -s NP_001034065.1 66 265 + 471 LVALLLIVLPMVFSPAHSCGPGRGLGRHRA--RNLYPLVLKQTIPNLSEYTNSASGPLEGVIRRDSPKFKDLVPNYNRDILFRDEEGTGADRLMSKRCKEKLNVLAYSVMNEWPGIRLLVTESWDEDYHHGQESLHYEGRAVTIATSDRDQSKYGMLARLAVEAGFDWVSYVSRRHIYCSVKSDSSISSHVHGCFTPESTALLESGVRKPLGELSIGDRVLSMTANGQAVYSEVILFMDRNLEQMQNFVQLHT-DGGAVLTVTPAHLV - -a score=131 EG2=0.4 E=4.1e-14 -s NP_002172.2 293 95 + 411 FASHVQPGQYVLVAGVPG--LQPARVAAVSTHVALGAYAPLTKHGTLVVEDVVASCFAAVADHHLAQLAFWPLRLFHSLAWGSWTPG-EGVHWYPQLL -s NP_001034065.1 344 96 + 471 FADRIEEKNQVLVRDVETGELRPQRVVKVGSVRSKGVVAPLTREGTIVVNSVAASCYAVINSQSLAHWGLAPMRLLSTLE--AWLPAKEQLHSSPKVV - -a score=41 EG2=3.7e+11 E=0.06 -s NP_002172.2 91 34 + 411 KDEENTGADRLMTQRCKDRLNSLAISVMNQWPGV -s NP_001034065.1 44 34 + 471 QEETQTMRHIAHTQRCLSRLTSLVALLLIVLPMV - -a score=30 EG2=1.1e+13 E=1.8 -s NP_002172.2 180 18 + 411 ESKAHVHCSVKSEHSAAA -s NP_001034065.1 20 18 + 471 DAKCHSSSSSSSSKSAAS - -a score=24 EG2=6.6e+13 E=12 -s NP_002172.2 26 23 + 411 GCGPGRVVGSRRRPPRKLVPLAY -s NP_001034065.1 150 21 + 471 GTGADRLMSKRCK--EKLNVLAY - -a score=24 EG2=6.6e+13 E=12 -s NP_002172.2 106 27 + 411 CKDRLNSLAISVMNQWPGVKLRVTEGW -s NP_001034065.1 399 27 + 471 CYAVINSQSLAHWGLAPMRLLSTLEAW - # Query sequences=1 |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/last_split.maf --- a/test-data/last_split.maf Fri Nov 13 09:05:49 2020 +0000 +++ b/test-data/last_split.maf Wed Mar 24 22:36:50 2021 +0000 |
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| @@ -1,8 +1,8 @@ -# LAST version 1021 +# LAST version 1205 # # a=7 b=1 A=7 B=1 e=22 d=13 x=21 y=9 z=21 D=1e+06 # R=10 u=0 s=2 S=0 M=0 T=0 m=10 l=1 L=999999999 n=10 k=1 w=1000 t=2.82533 j=3 Q=0 -# ref_db +# /home/berntm/.planemo/planemo_tmp_3z8peizh/test-data/humdb # Reference sequences=1 normal letters=16571 # # A R N D C Q E G H I L K M F P S T W Y V B J Z X * @@ -89,7 +89,7 @@ s fuguMito 16146 196 + 16447 A-----GTGC---AGCGC-----GTCAATGGTTCA-TCAAGGTTGAA-CAT---TTTTTCT-TGGTTTATGGTA---ATGTTAATTAATGAATTAAGACAT---TATTTAAG------AATTACATTACTGATATCAAGGACATAA--ATAATAATACGAT-TCAACAATCATACAATTTCAcccccttcttctttttaaaaaaatt-aacgtataccccccctacccccc p 333333336?????@@@@@@@@@@@@@@@@@@@@@@@@@@@@AAAAAABBBBBBCCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDEEEEEEEEEEEEEEEEEEEEEEDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEED@@: -a score=255 mismap=0.516 acc=AG +a score=255 mismap=0.515 acc=AG s humanMito 2030 114 + 16571 ATAGAATCTTAGTTCAA-CTTTAAATTTG-CCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTCCAAAGAGGAACAGCTCTTTGGACACTAGGA-AAAAACCTTGTA s fuguMito 16342 104 + 16447 ctaAAAAATAGGAGAGACCTTTAAGTTTGAACCA-AG----CTCT----CCActt----aattaaatattcatcatattattatcatatattataatattataataatataattata p ##################################################################################################################### |
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| diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/last_train.txt --- a/test-data/last_train.txt Fri Nov 13 09:05:49 2020 +0000 +++ b/test-data/last_train.txt Wed Mar 24 22:36:50 2021 +0000 |
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| b'@@ -1,43 +1,43 @@\n-# lastal version: 1021\n+# lastal version: 1205\n # maximum percent identity: 100\n # scale of score parameters: 4.5512\n # scale used while training: 91.024\n \n-# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84\n+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco\n \n-# aligned letter pairs: 14938.3\n-# deletes: 664.27\n-# inserts: 839.49\n-# delOpens: 344.82\n-# insOpens: 404.93\n+# aligned letter pairs: 14938.4\n+# deletes: 664.28\n+# inserts: 839.52\n+# delOpens: 344.93\n+# insOpens: 404.94\n # alignments: 3\n-# mean delete size: 1.92643\n-# mean insert size: 2.07317\n-# matchProb: 0.951966\n-# delOpenProb: 0.0219742\n-# insOpenProb: 0.0258048\n-# delExtendProb: 0.480904\n-# insExtendProb: 0.517648\n+# mean delete size: 1.92584\n+# mean insert size: 2.0732\n+# matchProb: 0.951959\n+# delOpenProb: 0.0219809\n+# insOpenProb: 0.0258051\n+# delExtendProb: 0.480746\n+# insExtendProb: 0.517653\n \n-# substitution percent identity: 71.9318\n+# substitution percent identity: 71.9301\n \n # count matrix (query letters = columns, reference letters = rows):\n # A C G T \n-# A 3296.3 533.237 387.81 392.24 \n-# C 553.59 3241.5 182.39 686.22 \n-# G 232.54 102.399 1565.4 84.91 \n-# T 335.173 558.68 147.16 2651 \n+# A 3296.3 533.242 387.82 392.35 \n+# C 553.59 3241.5 182.39 686.23 \n+# G 232.64 102.401 1565.4 84.91 \n+# T 335.174 558.781 147.17 2651 \n \n # probability matrix (query letters = columns, reference letters = rows):\n # A C G T \n-# A 0.22048 0.0356667 0.0259395 0.0262358 \n-# C 0.0370281 0.216815 0.0121996 0.0458993 \n-# G 0.0155539 0.00684918 0.104705 0.00567939 \n-# T 0.0224188 0.0373685 0.00984312 0.177318 \n+# A 0.220475 0.0356662 0.0259396 0.0262426 \n+# C 0.0370272 0.21681 0.0121993 0.0458989 \n+# G 0.0155603 0.00684915 0.104703 0.00567926 \n+# T 0.0224183 0.0373744 0.00984356 0.177314 \n \n-# delExistCost: 343\n+# delExistCost: 342\n # insExistCost: 341\n-# delExtendCost: 64\n+# delExtendCost: 65\n # insExtendCost: 58\n \n # score matrix (query letters = columns, reference letters = rows):\n@@ -47,84 +47,84 @@\n # G -89 -164 145 -167\n # T -112 -66 -127 90\n \n-# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.3148 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84\n+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1872 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco\n \n-# aligned letter pairs: 14338.3\n-# deletes: 327.44\n-# inserts: 474.13\n-# delOpens: 166.73\n-# insOpens: 216.45\n+# aligned letter pairs: 14397.9\n+# deletes: 322.93\n+# inserts: 481.67\n+# delOpens: 166.26\n+# insOpens: 218.88\n # alignments: 10\n-# mean delete size: 1.96389\n-# mean insert size: 2.19048\n-# matchProb: 0.973244\n-# delOpenProb: 0.0113172\n-# insOpenProb: 0.014692\n-# delExtendProb: 0.490807\n-# insExtendProb: 0.54348\n+# mean delete size: 1.94232\n+# mean insert size: 2.20061\n+# matchProb: 0.973223\n+# delOpenProb: 0.0112383\n+# insOpenProb: 0.0147951\n+# delExtendProb: 0.485152\n+# insExtendProb: 0.545581\n \n-# substitution percent identity: 70.6019\n+# substitution percent identity: 70.5263\n \n # count matrix (query letters = columns, reference letters = rows):\n # A C G T \n-# A 3076.4 546.106 412.41 369.93 \n'..b' G T \n-# A 3081.6 634.732 445.81 423.98 \n+# A 3081.6 633.732 445.81 423.98 \n # C 650.18 2986.2 169.39 816.1 \n # G 273.05 94.134 1561.4 71.9 \n-# T 365.574 674.07 131.782 2531.4 \n+# T 365.574 674.17 131.782 2531.4 \n \n # probability matrix (query letters = columns, reference letters = rows):\n # A C G T \n-# A 0.206662 0.0425672 0.0298975 0.0284335 \n-# C 0.0436032 0.200264 0.0113598 0.0547303 \n-# G 0.0183116 0.00631293 0.104713 0.00482185 \n-# T 0.0245166 0.0452053 0.00883773 0.169764 \n+# A 0.206675 0.0425027 0.0298993 0.0284352 \n+# C 0.0436058 0.200276 0.0113605 0.0547336 \n+# G 0.0183127 0.00631331 0.104719 0.00482214 \n+# T 0.0245181 0.0452147 0.00883826 0.169774 \n \n-# delExistCost: 587\n+# delExistCost: 586\n # insExistCost: 541\n # delExtendCost: 32\n # insExtendCost: 30\n@@ -399,37 +399,37 @@\n # G -71 -168 146 -180\n # T -100 -45 -135 88\n \n-# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4821 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84\n+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.494 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco\n \n # aligned letter pairs: 14897.4\n-# deletes: 189.355\n-# inserts: 357.265\n-# delOpens: 56.08\n-# insOpens: 100.658\n+# deletes: 190.558\n+# inserts: 358.367\n+# delOpens: 56.231\n+# insOpens: 100.769\n # alignments: 5\n-# mean delete size: 3.37652\n-# mean insert size: 3.5493\n-# matchProb: 0.989194\n-# delOpenProb: 0.00372374\n-# insOpenProb: 0.00668374\n-# delExtendProb: 0.703837\n-# insExtendProb: 0.718254\n+# mean delete size: 3.38884\n+# mean insert size: 3.55632\n+# matchProb: 0.989177\n+# delOpenProb: 0.0037337\n+# insOpenProb: 0.00669099\n+# delExtendProb: 0.704914\n+# insExtendProb: 0.718811\n \n-# substitution percent identity: 68.1453\n+# substitution percent identity: 68.1458\n \n # count matrix (query letters = columns, reference letters = rows):\n # A C G T \n-# A 3081.6 633.731 445.81 423.98 \n+# A 3081.6 633.732 445.81 423.98 \n # C 650.08 2986.2 169.39 816.1 \n-# G 273.05 94.136 1561.4 71.9 \n-# T 365.674 674.07 131.672 2531.4 \n+# G 273.05 94.125 1561.4 71.9 \n+# T 365.574 674.07 131.672 2531.4 \n \n # probability matrix (query letters = columns, reference letters = rows):\n # A C G T \n-# A 0.206677 0.0425032 0.0298997 0.0284356 \n-# C 0.0435997 0.200279 0.0113607 0.0547344 \n-# G 0.018313 0.00631353 0.10472 0.0048222 \n-# T 0.0245251 0.0452087 0.00883101 0.169776 \n+# A 0.206679 0.0425036 0.0298999 0.0284358 \n+# C 0.0436 0.200281 0.0113608 0.0547348 \n+# G 0.0183131 0.00631284 0.104721 0.00482224 \n+# T 0.0245186 0.045209 0.00883107 0.169778 \n \n # delExistCost: 588\n # insExistCost: 541\n@@ -443,7 +443,7 @@\n # G -71 -168 146 -180\n # T -100 -45 -135 88\n \n-# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4704 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84\n+# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4704 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco\n \n # aligned letter pairs: 14897.4\n # deletes: 188.951\n' |
| b |
| diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/last_train_E.txt --- a/test-data/last_train_E.txt Fri Nov 13 09:05:49 2020 +0000 +++ b/test-data/last_train_E.txt Wed Mar 24 22:36:50 2021 +0000 |
| b |
| b'@@ -1,9 +1,9 @@\n-# lastal version: 1021\n+# lastal version: 1205\n # maximum percent identity: 100\n # scale of score parameters: 4.5512\n # scale used while training: 91.024\n \n-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB\n+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3\n \n # aligned letter pairs: 14901\n # deletes: 694\n@@ -47,7 +47,7 @@\n # G -88 -164 145 -167\n # T -112 -66 -127 90\n \n-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4322 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB\n+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4322 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3\n \n # aligned letter pairs: 14771\n # deletes: 379.3\n@@ -63,21 +63,21 @@\n # delExtendProb: 0.511732\n # insExtendProb: 0.566038\n \n-# substitution percent identity: 70.0105\n+# substitution percent identity: 70.0152\n \n # count matrix (query letters = columns, reference letters = rows):\n # A C G T \n-# A 3158 583.4 429.9 391.6 \n+# A 3158 582.4 429.9 391.6 \n # C 589 3065 156.8 774 \n # G 252.2 88.64 1571 68.46 \n # T 342.6 630.1 131.09 2566 \n \n # probability matrix (query letters = columns, reference letters = rows):\n # A C G T \n-# A 0.21341 0.0394248 0.0290516 0.0264634 \n-# C 0.0398032 0.207126 0.0105962 0.0523051 \n-# G 0.0170431 0.00599008 0.106165 0.00462637 \n-# T 0.0231521 0.0425807 0.00885876 0.173404 \n+# A 0.213425 0.0393599 0.0290536 0.0264652 \n+# C 0.0398059 0.20714 0.0105969 0.0523086 \n+# G 0.0170442 0.00599049 0.106172 0.00462668 \n+# T 0.0231537 0.0425836 0.00885935 0.173416 \n \n # delExistCost: 406\n # insExistCost: 400\n@@ -86,218 +86,218 @@\n \n # score matrix (query letters = columns, reference letters = rows):\n # A C G T\n-# A 75 -79 -48 -102\n+# A 76 -79 -48 -102\n # C -78 72 -140 -41\n # G -79 -174 146 -185\n # T -107 -52 -136 89\n \n-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.8564 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB\n+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.6863 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3\n \n # aligned letter pairs: 14881\n-# deletes: 258.8\n-# inserts: 446.1\n-# delOpens: 112.91\n-# insOpens: 168\n+# deletes: 264.3\n+# inserts: 451.9\n+# delOpens: 116.18\n+# insOpens: 171.3\n # alignments: 2\n-# mean delete size: 2.29209\n-# mean insert size: 2.65536\n-# matchProb: 0.981278\n-# delOpenProb: 0.00744548\n-# insOpenProb: 0.0110782\n-# delExtendProb: 0.563717\n-# insExtendProb: 0.623403\n+# mean delete size: 2.27492\n+# mean insert size: 2.63806\n+# matchProb: 0.980854\n+# delOpenProb: 0.00765779\n+# insOpenProb: 0.0112909\n+# delExtendProb: 0.560424\n+# insExtendProb: 0.620934\n \n-# substitution percent identity: 68.9366\n+# substitution percent identity: 68.9602\n \n # count matrix (query letters = columns, reference letters = rows):\n # A C G T \n-# A 3126 618.3 445 406.6 \n-# C 622.8 3041 159.4 805.4 \n-# G 265.2 91.16 1560 68.22 \n-# T 357.3 660 133.33 2554 \n+# A 3126 617.2 445 406.6 \n+# C 621.9 3041 159.4 804.4 \n+# G 264.2 '..b'3133 0.00905532 0.169074 \n+# A 0.206519 0.0433937 0.0301199 0.0285508 \n+# C 0.043801 0.200176 0.0113442 0.0548447 \n+# G 0.0182816 0.00639321 0.103493 0.00477137 \n+# T 0.0248851 0.04531 0.00905532 0.169061 \n+\n+# delExistCost: 587\n+# insExistCost: 543\n+# delExtendCost: 32\n+# insExtendCost: 29\n+\n+# score matrix (query letters = columns, reference letters = rows):\n+# A C G T\n+# A 74 -68 -42 -94\n+# C -68 70 -132 -35\n+# G -70 -166 147 -180\n+# T -99 -45 -132 88\n+\n+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2049 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3\n+\n+# aligned letter pairs: 14981\n+# deletes: 195.9\n+# inserts: 384.7\n+# delOpens: 57.66\n+# insOpens: 104.5\n+# alignments: 2\n+# mean delete size: 3.3975\n+# mean insert size: 3.68134\n+# matchProb: 0.989096\n+# delOpenProb: 0.00380691\n+# insOpenProb: 0.00689944\n+# delExtendProb: 0.705666\n+# insExtendProb: 0.72836\n+\n+# substitution percent identity: 67.9195\n+\n+# count matrix (query letters = columns, reference letters = rows):\n+# A C G T \n+# A 3093 649.9 451.2 427.6 \n+# C 656.1 2998 169.9 821.4 \n+# G 273.8 95.74 1550 71.46 \n+# T 373.7 678.6 135.62 2532 \n+\n+# probability matrix (query letters = columns, reference letters = rows):\n+# A C G T \n+# A 0.206503 0.0433902 0.0301241 0.0285485 \n+# C 0.0438042 0.20016 0.0113433 0.0548404 \n+# G 0.0182801 0.00639203 0.103485 0.00477099 \n+# T 0.0249499 0.0453064 0.0090546 0.169048 \n+\n+# delExistCost: 586\n+# insExistCost: 543\n+# delExtendCost: 32\n+# insExtendCost: 29\n+\n+# score matrix (query letters = columns, reference letters = rows):\n+# A C G T\n+# A 74 -68 -42 -94\n+# C -68 70 -132 -35\n+# G -70 -166 147 -180\n+# T -99 -45 -132 88\n+\n+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2167 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3\n+\n+# aligned letter pairs: 14981\n+# deletes: 196\n+# inserts: 384.7\n+# delOpens: 57.87\n+# insOpens: 104.51\n+# alignments: 2\n+# mean delete size: 3.3869\n+# mean insert size: 3.68099\n+# matchProb: 0.989081\n+# delOpenProb: 0.00382071\n+# insOpenProb: 0.0069\n+# delExtendProb: 0.704745\n+# insExtendProb: 0.728334\n+\n+# substitution percent identity: 67.9245\n+\n+# count matrix (query letters = columns, reference letters = rows):\n+# A C G T \n+# A 3093 649.9 451.2 427.6 \n+# C 656.1 2998 169.9 821.4 \n+# G 273.8 95.64 1550 71.46 \n+# T 372.7 678.6 135.62 2532 \n+\n+# probability matrix (query letters = columns, reference letters = rows):\n+# A C G T \n+# A 0.206518 0.0433934 0.0301264 0.0285506 \n+# C 0.0438074 0.200175 0.0113441 0.0548444 \n+# G 0.0182815 0.00638583 0.103493 0.00477134 \n+# T 0.024885 0.0453097 0.00905527 0.16906 \n \n # delExistCost: 586\n # insExistCost: 543\n@@ -443,7 +575,7 @@\n # G -70 -166 147 -180\n # T -99 -45 -132 88\n \n-# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0834 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB\n+# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0834 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3\n \n # aligned letter pairs: 14981\n # deletes: 196\n' |