| Previous changeset 12:832c20329690 (2018-04-23) Next changeset 14:2e0fb4bc860e (2019-01-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753 |
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modified:
emboss_antigenic.xml emboss_backtranseq.xml emboss_banana.xml emboss_biosed.xml emboss_btwisted.xml emboss_cai.xml emboss_cai_custom.xml emboss_chaos.xml emboss_charge.xml emboss_checktrans.xml emboss_chips.xml emboss_cirdna.xml emboss_codcmp.xml emboss_coderet.xml emboss_compseq.xml emboss_cpgplot.xml emboss_cpgreport.xml emboss_cusp.xml emboss_cutseq.xml emboss_dan.xml emboss_degapseq.xml emboss_descseq.xml emboss_diffseq.xml emboss_digest.xml emboss_dotmatcher.xml emboss_dotpath.xml emboss_dottup.xml emboss_dreg.xml emboss_einverted.xml emboss_epestfind.xml emboss_equicktandem.xml emboss_est2genome.xml emboss_etandem.xml emboss_extractfeat.xml emboss_extractseq.xml emboss_freak.xml emboss_fuzzpro.xml emboss_fuzztran.xml emboss_garnier.xml emboss_geecee.xml emboss_getorf.xml emboss_helixturnhelix.xml emboss_hmoment.xml emboss_iep.xml emboss_infoseq.xml emboss_isochore.xml emboss_lindna.xml emboss_marscan.xml emboss_maskfeat.xml emboss_maskseq.xml emboss_matcher.xml emboss_megamerger.xml emboss_merger.xml emboss_msbar.xml emboss_needle.xml emboss_newcpgreport.xml emboss_newcpgseek.xml emboss_newseq.xml emboss_noreturn.xml emboss_notseq.xml emboss_nthseq.xml emboss_octanol.xml emboss_oddcomp.xml emboss_palindrome.xml emboss_pasteseq.xml emboss_patmatdb.xml emboss_pepcoil.xml emboss_pepinfo.xml emboss_pepnet.xml emboss_pepstats.xml emboss_pepwheel.xml emboss_pepwindow.xml emboss_pepwindowall.xml emboss_plotcon.xml emboss_plotorf.xml emboss_polydot.xml emboss_preg.xml emboss_prettyplot.xml emboss_prettyseq.xml emboss_primersearch.xml emboss_revseq.xml emboss_seqmatchall.xml emboss_seqret.xml emboss_showfeat.xml emboss_shuffleseq.xml emboss_sigcleave.xml emboss_sirna.xml emboss_sixpack.xml emboss_skipseq.xml emboss_splitter.xml emboss_supermatcher.xml emboss_syco.xml emboss_tcode.xml emboss_textsearch.xml emboss_tmap.xml emboss_tranalign.xml emboss_transeq.xml emboss_trimest.xml emboss_trimseq.xml emboss_twofeat.xml emboss_union.xml emboss_vectorstrip.xml emboss_water.xml emboss_wobble.xml emboss_wordcount.xml emboss_wordmatch.xml macros.xml test-data/emboss_sixpack_out2.sixpack |
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added:
test-data/emboss_sixpack_out.fasta |
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| diff -r 832c20329690 -r 8992d258e42f emboss_antigenic.xml --- a/emboss_antigenic.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_antigenic.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: antigenic1" name="antigenic" version="5.0.0.1"> +<tool id="EMBOSS: antigenic1" name="antigenic" version="@VERSION@.1"> <description>Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_backtranseq.xml --- a/emboss_backtranseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_backtranseq.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: backtranseq2" name="backtranseq" version="5.0.0"> +<tool id="EMBOSS: backtranseq2" name="backtranseq" version="@VERSION@"> <description>Back translate a protein sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_banana.xml --- a/emboss_banana.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_banana.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: banana3" name="banana" version="5.0.0"> +<tool id="EMBOSS: banana3" name="banana" version="@VERSION@"> <description>Bending and curvature plot in B-DNA</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_biosed.xml --- a/emboss_biosed.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_biosed.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: biosed4" name="biosed" version="5.0.0"> +<tool id="EMBOSS: biosed4" name="biosed" version="@VERSION@"> <description>Replace or delete sequence sections</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_btwisted.xml --- a/emboss_btwisted.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_btwisted.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: btwisted5" name="btwisted" version="5.0.0"> +<tool id="EMBOSS: btwisted5" name="btwisted" version="@VERSION@"> <description>Calculates the twisting in a B-DNA sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_cai.xml --- a/emboss_cai.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_cai.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: cai6" name="cai" version="5.0.0"> +<tool id="EMBOSS: cai6" name="cai" version="@VERSION@"> <description>CAI codon adaptation index</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_cai_custom.xml --- a/emboss_cai_custom.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_cai_custom.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: cai_custom6" name="cai custom" version="5.0.0"> +<tool id="EMBOSS: cai_custom6" name="cai custom" version="@VERSION@"> <description>CAI codon adaptation index using custom codon usage file</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_chaos.xml --- a/emboss_chaos.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_chaos.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: chaos7" name="chaos" version="5.0.0"> +<tool id="EMBOSS: chaos7" name="chaos" version="@VERSION@"> <description>Create a chaos game representation plot for a sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_charge.xml --- a/emboss_charge.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_charge.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: charge8" name="charge" version="5.0.0.1"> +<tool id="EMBOSS: charge8" name="charge" version="@VERSION@.1"> <description>Protein charge plot</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_checktrans.xml --- a/emboss_checktrans.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_checktrans.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0.1"> +<tool id="EMBOSS: checktrans9" name="checktrans" version="@VERSION@.1"> <description>Reports STOP codons and ORF statistics of a protein</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_chips.xml --- a/emboss_chips.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_chips.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: chips10" name="chips" version="5.0.0"> +<tool id="EMBOSS: chips10" name="chips" version="@VERSION@"> <description>Codon usage statistics</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_cirdna.xml --- a/emboss_cirdna.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_cirdna.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: cirdna11" name="cirdna" version="5.0.0"> +<tool id="EMBOSS: cirdna11" name="cirdna" version="@VERSION@"> <description>Draws circular maps of DNA constructs</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_codcmp.xml --- a/emboss_codcmp.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_codcmp.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: codcmp12" name="codcmp" version="5.0.0"> +<tool id="EMBOSS: codcmp12" name="codcmp" version="@VERSION@"> <description>Codon usage table comparison</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_coderet.xml --- a/emboss_coderet.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_coderet.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: coderet13" name="coderet" version="5.0.0"> +<tool id="EMBOSS: coderet13" name="coderet" version="@VERSION@"> <description>Extract CDS, mRNA and translations from feature tables</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_compseq.xml --- a/emboss_compseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_compseq.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: compseq14" name="compseq" version="5.0.0.1"> +<tool id="EMBOSS: compseq14" name="compseq" version="@VERSION@.1"> <description>Count composition of dimer/trimer/etc words in a sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_cpgplot.xml --- a/emboss_cpgplot.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_cpgplot.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0"> +<tool id="EMBOSS: cpgplot15" name="cpgplot" version="@VERSION@"> <description>Plot CpG rich areas</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_cpgreport.xml --- a/emboss_cpgreport.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_cpgreport.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0.1"> +<tool id="EMBOSS: cpgreport16" name="cpgreport" version="@VERSION@.1"> <description>Reports all CpG rich regions</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_cusp.xml --- a/emboss_cusp.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_cusp.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: cusp17" name="cusp" version="5.0.0"> +<tool id="EMBOSS: cusp17" name="cusp" version="@VERSION@"> <description>Create a codon usage table</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_cutseq.xml --- a/emboss_cutseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_cutseq.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: cutseq18" name="cutseq" version="5.0.0.1"> +<tool id="EMBOSS: cutseq18" name="cutseq" version="@VERSION@.1"> <description>Removes a specified section from a sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_dan.xml --- a/emboss_dan.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_dan.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: dan19" name="dan" version="5.0.0.1"> +<tool id="EMBOSS: dan19" name="dan" version="@VERSION@.1"> <description>Calculates DNA RNA/DNA melting temperature</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_degapseq.xml --- a/emboss_degapseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_degapseq.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: degapseq20" name="degapseq" version="5.0.0"> +<tool id="EMBOSS: degapseq20" name="degapseq" version="@VERSION@"> <description>Removes gap characters from sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_descseq.xml --- a/emboss_descseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_descseq.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: descseq21" name="descseq" version="5.0.0"> +<tool id="EMBOSS: descseq21" name="descseq" version="@VERSION@"> <description>Alter the name or description of a sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_diffseq.xml --- a/emboss_diffseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_diffseq.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0.1"> +<tool id="EMBOSS: diffseq22" name="diffseq" version="@VERSION@.1"> <description>Find differences between nearly identical sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_digest.xml --- a/emboss_digest.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_digest.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: digest23" name="digest" version="5.0.0"> +<tool id="EMBOSS: digest23" name="digest" version="@VERSION@"> <description>Protein proteolytic enzyme or reagent cleavage digest</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_dotmatcher.xml --- a/emboss_dotmatcher.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_dotmatcher.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: dotmatcher24" name="dotmatcher" version="5.0.0.1"> +<tool id="EMBOSS: dotmatcher24" name="dotmatcher" version="@VERSION@.1"> <description>Displays a thresholded dotplot of two sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_dotpath.xml --- a/emboss_dotpath.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_dotpath.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: dotpath25" name="dotpath" version="5.0.0.1"> +<tool id="EMBOSS: dotpath25" name="dotpath" version="@VERSION@.1"> <description>Non-overlapping wordmatch dotplot of two sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_dottup.xml --- a/emboss_dottup.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_dottup.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: dottup26" name="dottup" version="5.0.0.1"> +<tool id="EMBOSS: dottup26" name="dottup" version="@VERSION@.1"> <description>Displays a wordmatch dotplot of two sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_dreg.xml --- a/emboss_dreg.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_dreg.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: dreg27" name="dreg" version="5.0.0"> +<tool id="EMBOSS: dreg27" name="dreg" version="@VERSION@"> <description>Regular expression search of a nucleotide sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_einverted.xml --- a/emboss_einverted.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_einverted.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: einverted28" name="einverted" version="5.0.0.1"> +<tool id="EMBOSS: einverted28" name="einverted" version="@VERSION@.1"> <description>Finds DNA inverted repeats</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_epestfind.xml --- a/emboss_epestfind.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_epestfind.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0.1"> +<tool id="EMBOSS: epestfind29" name="epestfind" version="@VERSION@.1"> <description>Finds PEST motifs as potential proteolytic cleavage sites</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_equicktandem.xml --- a/emboss_equicktandem.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_equicktandem.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: equicktandem31" name="equicktandem" version="5.0.0.1"> +<tool id="EMBOSS: equicktandem31" name="equicktandem" version="@VERSION@.1"> <description>Finds tandem repeats</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_est2genome.xml --- a/emboss_est2genome.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_est2genome.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0.1"> +<tool id="EMBOSS: est2genome32" name="est2genome" version="@VERSION@.1"> <description>Align EST and genomic DNA sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_etandem.xml --- a/emboss_etandem.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_etandem.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: etandem33" name="etandem" version="5.0.0.1"> +<tool id="EMBOSS: etandem33" name="etandem" version="@VERSION@.1"> <description>Looks for tandem repeats in a nucleotide sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_extractfeat.xml --- a/emboss_extractfeat.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_extractfeat.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: extractfeat34" name="extractfeat" version="5.0.0.1"> +<tool id="EMBOSS: extractfeat34" name="extractfeat" version="@VERSION@.1"> <!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences --> <description>Extract features from a sequence</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_extractseq.xml --- a/emboss_extractseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_extractseq.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: extractseq35" name="extractseq" version="5.0.0"> +<tool id="EMBOSS: extractseq35" name="extractseq" version="@VERSION@"> <description>Extract regions from a sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_freak.xml --- a/emboss_freak.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_freak.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: freak36" name="freak" version="5.0.0.1"> +<tool id="EMBOSS: freak36" name="freak" version="@VERSION@.1"> <description>Residue/base frequency table or plot</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_fuzzpro.xml --- a/emboss_fuzzpro.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_fuzzpro.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: fuzzpro38" name="fuzzpro" version="5.0.0.1"> +<tool id="EMBOSS: fuzzpro38" name="fuzzpro" version="@VERSION@.1"> <description>Protein pattern search</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_fuzztran.xml --- a/emboss_fuzztran.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_fuzztran.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0.1"> +<tool id="EMBOSS: fuzztran39" name="fuzztran" version="@VERSION@.1"> <description>Protein pattern search after translation</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_garnier.xml --- a/emboss_garnier.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_garnier.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: garnier40" name="garnier" version="5.0.0"> +<tool id="EMBOSS: garnier40" name="garnier" version="@VERSION@"> <description>Predicts protein secondary structure</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_geecee.xml --- a/emboss_geecee.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_geecee.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: geecee41" name="geecee" version="5.0.0"> +<tool id="EMBOSS: geecee41" name="geecee" version="@VERSION@"> <description>Calculates fractional GC content of nucleic acid sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_getorf.xml --- a/emboss_getorf.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_getorf.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: getorf42" name="getorf" version="5.0.0.1"> +<tool id="EMBOSS: getorf42" name="getorf" version="@VERSION@.1"> <description>Finds and extracts open reading frames (ORFs)</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_helixturnhelix.xml --- a/emboss_helixturnhelix.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_helixturnhelix.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: helixturnhelix43" name="helixturnhelix" version="5.0.0.1"> +<tool id="EMBOSS: helixturnhelix43" name="helixturnhelix" version="@VERSION@.1"> <description>Report nucleic acid binding motifs</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_hmoment.xml --- a/emboss_hmoment.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_hmoment.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: hmoment44" name="hmoment" version="5.0.0.1"> +<tool id="EMBOSS: hmoment44" name="hmoment" version="@VERSION@.1"> <description>Hydrophobic moment calculation</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_iep.xml --- a/emboss_iep.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_iep.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: iep45" name="iep" version="5.0.0.1"> +<tool id="EMBOSS: iep45" name="iep" version="@VERSION@.1"> <description>Calculates the isoelectric point of a protein</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_infoseq.xml --- a/emboss_infoseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_infoseq.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: infoseq46" name="infoseq" version="5.0.0"> +<tool id="EMBOSS: infoseq46" name="infoseq" version="@VERSION@"> <!-- info contains file information always --> <description>Displays some simple information about sequences</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_isochore.xml --- a/emboss_isochore.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_isochore.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: isochore47" name="isochore" version="5.0.0.1"> +<tool id="EMBOSS: isochore47" name="isochore" version="@VERSION@.1"> <description>Plots isochores in large DNA sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_lindna.xml --- a/emboss_lindna.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_lindna.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: lindna48" name="lindna" version="5.0.0.1"> +<tool id="EMBOSS: lindna48" name="lindna" version="@VERSION@.1"> <!-- tool produces memory error in ajmem.c --> <description>Draws linear maps of DNA constructs</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_marscan.xml --- a/emboss_marscan.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_marscan.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: marscan49" name="marscan" version="5.0.0"> +<tool id="EMBOSS: marscan49" name="marscan" version="@VERSION@"> <description>Finds MAR/SAR sites in nucleic sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_maskfeat.xml --- a/emboss_maskfeat.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_maskfeat.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: maskfeat50" name="maskfeat" version="5.0.0"> +<tool id="EMBOSS: maskfeat50" name="maskfeat" version="@VERSION@"> <description>Mask off features of a sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_maskseq.xml --- a/emboss_maskseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_maskseq.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: maskseq51" name="maskseq" version="5.0.0"> +<tool id="EMBOSS: maskseq51" name="maskseq" version="@VERSION@"> <description>Mask off regions of a sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_matcher.xml --- a/emboss_matcher.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_matcher.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: matcher52" name="matcher" version="5.0.0.1"> +<tool id="EMBOSS: matcher52" name="matcher" version="@VERSION@.1"> <description>Finds the best local alignments between two sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_megamerger.xml --- a/emboss_megamerger.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_megamerger.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: megamerger53" name="megamerger" version="5.0.0.1"> +<tool id="EMBOSS: megamerger53" name="megamerger" version="@VERSION@.1"> <description>Merge two large overlapping nucleic acid sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_merger.xml --- a/emboss_merger.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_merger.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: merger54" name="merger" version="5.0.0.1"> +<tool id="EMBOSS: merger54" name="merger" version="@VERSION@.1"> <description>Merge two overlapping nucleic acid sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_msbar.xml --- a/emboss_msbar.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_msbar.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: msbar55" name="msbar" version="5.0.0.1"> +<tool id="EMBOSS: msbar55" name="msbar" version="@VERSION@.1"> <description>Mutate sequence beyond all recognition</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_needle.xml --- a/emboss_needle.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_needle.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: needle56" name="needle" version="5.0.0.1"> +<tool id="EMBOSS: needle56" name="needle" version="@VERSION@.1"> <description>Needleman-Wunsch global alignment</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_newcpgreport.xml --- a/emboss_newcpgreport.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_newcpgreport.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0.1"> +<tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="@VERSION@.1"> <description>Report CpG rich areas</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_newcpgseek.xml --- a/emboss_newcpgseek.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_newcpgseek.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: newcpgseek58" name="newcpgseek" version="5.0.0.1"> +<tool id="EMBOSS: newcpgseek58" name="newcpgseek" version="@VERSION@.1"> <description>Reports CpG rich region</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_newseq.xml --- a/emboss_newseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_newseq.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: newseq59" name="newseq" version="5.0.0"> +<tool id="EMBOSS: newseq59" name="newseq" version="@VERSION@"> <description>Type in a short new sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_noreturn.xml --- a/emboss_noreturn.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_noreturn.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: noreturn60" name="noreturn" version="5.0.0"> +<tool id="EMBOSS: noreturn60" name="noreturn" version="@VERSION@"> <description>Removes carriage return from ASCII files</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_notseq.xml --- a/emboss_notseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_notseq.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: notseq61" name="notseq" version="5.0.0"> +<tool id="EMBOSS: notseq61" name="notseq" version="@VERSION@"> <description>Exclude a set of sequences and write out the remaining ones</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_nthseq.xml --- a/emboss_nthseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_nthseq.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: nthseq62" name="nthseq" version="5.0.0.1"> +<tool id="EMBOSS: nthseq62" name="nthseq" version="@VERSION@.1"> <description>Writes one sequence from a multiple set of sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_octanol.xml --- a/emboss_octanol.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_octanol.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: octanol63" name="octanol" version="5.0.0.1"> +<tool id="EMBOSS: octanol63" name="octanol" version="@VERSION@.1"> <!-- graphics output with filename, no functional tests added --> <description>Displays protein hydropathy</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_oddcomp.xml --- a/emboss_oddcomp.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_oddcomp.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0.1"> +<tool id="EMBOSS: oddcomp64" name="oddcomp" version="@VERSION@.1"> <!-- output contains file location info, commented out functional tests --> <description>Find protein sequence regions with a biased composition</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_palindrome.xml --- a/emboss_palindrome.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_palindrome.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0.1"> +<tool id="EMBOSS: palindrome65" name="palindrome" version="@VERSION@.1"> <description>Looks for inverted repeats in a nucleotide sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_pasteseq.xml --- a/emboss_pasteseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_pasteseq.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: pasteseq66" name="pasteseq" version="5.0.0.1"> +<tool id="EMBOSS: pasteseq66" name="pasteseq" version="@VERSION@.1"> <description>Insert one sequence into another</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_patmatdb.xml --- a/emboss_patmatdb.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_patmatdb.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: patmatdb67" name="patmatdb" version="5.0.0"> +<tool id="EMBOSS: patmatdb67" name="patmatdb" version="@VERSION@"> <description>Search a protein sequence with a motif</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_pepcoil.xml --- a/emboss_pepcoil.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_pepcoil.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: pepcoil68" name="pepcoil" version="5.0.0.1"> +<tool id="EMBOSS: pepcoil68" name="pepcoil" version="@VERSION@.1"> <description>Predicts coiled coil regions</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_pepinfo.xml --- a/emboss_pepinfo.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_pepinfo.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: pepinfo69" name="pepinfo" version="5.0.0.1"> +<tool id="EMBOSS: pepinfo69" name="pepinfo" version="@VERSION@.1"> <!-- puts file info in output files --> <description>Plots simple amino acid properties in parallel</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_pepnet.xml --- a/emboss_pepnet.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_pepnet.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: pepnet70" name="pepnet" version="5.0.0"> +<tool id="EMBOSS: pepnet70" name="pepnet" version="@VERSION@"> <!-- graphical output file with path information --> <description>Displays proteins as a helical net</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_pepstats.xml --- a/emboss_pepstats.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_pepstats.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: pepstats71" name="pepstats" version="5.0.0"> +<tool id="EMBOSS: pepstats71" name="pepstats" version="@VERSION@"> <description>Protein statistics</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_pepwheel.xml --- a/emboss_pepwheel.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_pepwheel.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0.1"> +<tool id="EMBOSS: pepwheel72" name="pepwheel" version="@VERSION@.1"> <!-- produces png file --> <description>Shows protein sequences as helices</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_pepwindow.xml --- a/emboss_pepwindow.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_pepwindow.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: pepwindow73" name="pepwindow" version="5.0.0.1"> +<tool id="EMBOSS: pepwindow73" name="pepwindow" version="@VERSION@.1"> <!-- produces png file --> <description>Displays protein hydropathy</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_pepwindowall.xml --- a/emboss_pepwindowall.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_pepwindowall.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: pepwindowall74" name="pepwindowall" version="5.0.0.1"> +<tool id="EMBOSS: pepwindowall74" name="pepwindowall" version="@VERSION@.1"> <!-- produces png file --> <description>Displays protein hydropathy of a set of sequences</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_plotcon.xml --- a/emboss_plotcon.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_plotcon.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: plotcon75" name="plotcon" version="5.0.0.1"> +<tool id="EMBOSS: plotcon75" name="plotcon" version="@VERSION@.1"> <!-- produces png file --> <description>Plot quality of conservation of a sequence alignment</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_plotorf.xml --- a/emboss_plotorf.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_plotorf.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: plotorf76" name="plotorf" version="5.0.0"> +<tool id="EMBOSS: plotorf76" name="plotorf" version="@VERSION@"> <!-- produces png file output --> <description>Plot potential open reading frames</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_polydot.xml --- a/emboss_polydot.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_polydot.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: polydot77" name="polydot" version="5.0.0.1"> +<tool id="EMBOSS: polydot77" name="polydot" version="@VERSION@.1"> <!-- produces png file, not added functional tests --> <description>Displays all-against-all dotplots of a set of sequences</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_preg.xml --- a/emboss_preg.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_preg.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: preg78" name="preg" version="5.0.0"> +<tool id="EMBOSS: preg78" name="preg" version="@VERSION@"> <description>Regular expression search of a protein sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_prettyplot.xml --- a/emboss_prettyplot.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_prettyplot.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0.1"> +<tool id="EMBOSS: prettyplot79" name="prettyplot" version="@VERSION@.1"> <!-- produces png output with file name --> <description>Displays aligned sequences, with colouring and boxing</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_prettyseq.xml --- a/emboss_prettyseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_prettyseq.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: prettyseq80" name="prettyseq" version="5.0.0.1"> +<tool id="EMBOSS: prettyseq80" name="prettyseq" version="@VERSION@.1"> <description>Output sequence with translated ranges</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_primersearch.xml --- a/emboss_primersearch.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_primersearch.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: primersearch81" name="primersearch" version="5.0.0.1"> +<tool id="EMBOSS: primersearch81" name="primersearch" version="@VERSION@.1"> <description>Searches DNA sequences for matches with primer pairs</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_revseq.xml --- a/emboss_revseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_revseq.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: revseq82" name="revseq" version="5.0.0"> +<tool id="EMBOSS: revseq82" name="revseq" version="@VERSION@"> <description>Reverse and complement a sequence</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_seqmatchall.xml --- a/emboss_seqmatchall.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_seqmatchall.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: seqmatchall83" name="seqmatchall" version="5.0.0.1"> +<tool id="EMBOSS: seqmatchall83" name="seqmatchall" version="@VERSION@.1"> <description>All-against-all comparison of a set of sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_seqret.xml --- a/emboss_seqret.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_seqret.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: seqret84" name="seqret" version="5.0.0"> +<tool id="EMBOSS: seqret84" name="seqret" version="@VERSION@"> <description>Reads and writes sequences</description> <macros> <import>macros.xml</import> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_showfeat.xml --- a/emboss_showfeat.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_showfeat.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0.1"> +<tool id="EMBOSS: showfeat85" name="showfeat" version="@VERSION@.1"> <!-- tool gives memory errors --> <description>Show features of a sequence</description> <macros> |
| b |
| diff -r 832c20329690 -r 8992d258e42f emboss_shuffleseq.xml --- a/emboss_shuffleseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_shuffleseq.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: shuffleseq87" name="shuffleseq" version="5.0.0.1"> +<tool id="EMBOSS: shuffleseq87" name="shuffleseq" version="@VERSION@.1"> <!-- produces random outputs each time --> <description>Shuffles a set of sequences maintaining composition</description> <macros> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_sigcleave.xml --- a/emboss_sigcleave.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_sigcleave.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: sigcleave88" name="sigcleave" version="5.0.0.1"> +<tool id="EMBOSS: sigcleave88" name="sigcleave" version="@VERSION@.1"> <description>Reports protein signal cleavage sites</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_sirna.xml --- a/emboss_sirna.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_sirna.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: sirna89" name="sirna" version="5.0.0"> +<tool id="EMBOSS: sirna89" name="sirna" version="@VERSION@"> <description>Finds siRNA duplexes in mRNA</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_sixpack.xml --- a/emboss_sixpack.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_sixpack.xml Fri Jun 22 03:24:47 2018 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0.1"> +<tool id="EMBOSS: sixpack90" name="sixpack" version="@VERSION@+galaxy2"> <!-- tool adds file description and timestamp to output data --> <description>Display a DNA sequence with 6-frame translation and ORFs</description> <macros> @@ -6,8 +6,12 @@ </macros> <expand macro="requirements" /> <code file="emboss_format_corrector.py" /> - <command>sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase - '$uppercase' -number $number -width $width -length $length -margin $margin -name $disp_name -description $description -offset $offset -html $html_out1 -osformat $out_format2 -auto</command> + <command><![CDATA[ + sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize + #if str($uppercase): + -uppercase '$uppercase' + #end if + -number $number -width $width -length $length -margin $margin -name $disp_name -description $description -offset $offset -html $html_out1 -osformat $out_format2 -auto]]></command> <inputs> <param name="input1" type="data" format="fasta" label="Sequences" /> <param name="table" type="select" label="Code to use"> @@ -47,7 +51,7 @@ <option value="no">No</option> </param> <param name="orfminsize" type="integer" value="1" label="Minimum size of Open Reading Frames (ORFs) to display in the translations" /> - <param name="uppercase" type="text" value="" label="Regions to put in uppercase" /> + <param name="uppercase" type="text" value="" label="Regions to put in uppercase" help="If this is left blank, then the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-alpha-numeric character. Three examples of region specifications are: 1) 24-45, 56-78 2) 1:45, 67=99;765..888 3) 1,5,8,10,23,45,57,99"/> <param name="number" type="select" label="Number the sequence at the beginning and the end of each line"> <option value="yes">Yes</option> <option value="no">No</option> @@ -104,7 +108,7 @@ <data name="ofile1" format="sixpack" /> <data name="ofile2" format="fasta" /> </outputs> -<!-- <tests> + <tests> <test> <param name="input1" value="2.fasta"/> <param name="table" value="0"/> @@ -123,9 +127,10 @@ <param name="offset" value="1"/> <param name="html_out1" value="no"/> <param name="out_format2" value="fasta"/> + <output name="ofile1" file="emboss_sixpack_out2.sixpack" /> <output name="ofile2" file="emboss_sixpack_out.fasta"/> </test> - </tests> --> + </tests> <help> .. class:: warningmark |
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| diff -r 832c20329690 -r 8992d258e42f emboss_skipseq.xml --- a/emboss_skipseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_skipseq.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: skipseq91" name="skipseq" version="5.0.0.1"> +<tool id="EMBOSS: skipseq91" name="skipseq" version="@VERSION@.1"> <description>Reads and writes sequences, skipping first few</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_splitter.xml --- a/emboss_splitter.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_splitter.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: splitter92" name="splitter" version="5.0.0.1"> +<tool id="EMBOSS: splitter92" name="splitter" version="@VERSION@.1"> <description>Split a sequence into (overlapping) smaller sequences</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_supermatcher.xml --- a/emboss_supermatcher.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_supermatcher.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: supermatcher95" name="supermatcher" version="5.0.0.1"> +<tool id="EMBOSS: supermatcher95" name="supermatcher" version="@VERSION@.1"> <!-- puts file information in output report --> <description>Match large sequences against one or more other sequences</description> <macros> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_syco.xml --- a/emboss_syco.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_syco.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: syco96" name="syco" version="5.0.0.1"> +<tool id="EMBOSS: syco96" name="syco" version="@VERSION@.1"> <!-- graphics output --> <description>Synonymous codon usage Gribskov statistic plot</description> <macros> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_tcode.xml --- a/emboss_tcode.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_tcode.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: tcode97" name="tcode" version="5.0.0.1"> +<tool id="EMBOSS: tcode97" name="tcode" version="@VERSION@.1"> <description>Fickett TESTCODE statistic to identify protein-coding DNA</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_textsearch.xml --- a/emboss_textsearch.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_textsearch.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: textsearch98" name="textsearch" version="5.0.0"> +<tool id="EMBOSS: textsearch98" name="textsearch" version="@VERSION@"> <description>Search sequence documentation. Slow, use SRS and Entrez!</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_tmap.xml --- a/emboss_tmap.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_tmap.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: tmap99" name="tmap" version="5.0.0"> +<tool id="EMBOSS: tmap99" name="tmap" version="@VERSION@"> <description>Displays membrane spanning regions</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_tranalign.xml --- a/emboss_tranalign.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_tranalign.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0"> +<tool id="EMBOSS: tranalign100" name="tranalign" version="@VERSION@"> <description>Align nucleic coding regions given the aligned proteins</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_transeq.xml --- a/emboss_transeq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_transeq.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: transeq101" name="transeq" version="5.0.0"> +<tool id="EMBOSS: transeq101" name="transeq" version="@VERSION@"> <description>Translate nucleic acid sequences</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_trimest.xml --- a/emboss_trimest.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_trimest.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: trimest102" name="trimest" version="5.0.0.1"> +<tool id="EMBOSS: trimest102" name="trimest" version="@VERSION@.1"> <description>Trim poly-A tails off EST sequences</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_trimseq.xml --- a/emboss_trimseq.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_trimseq.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: trimseq103" name="trimseq" version="5.0.0.1"> +<tool id="EMBOSS: trimseq103" name="trimseq" version="@VERSION@.1"> <description>Trim ambiguous bits off the ends of sequences</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_twofeat.xml --- a/emboss_twofeat.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_twofeat.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0.1"> +<tool id="EMBOSS: twofeat104" name="twofeat" version="@VERSION@.1"> <description>Finds neighbouring pairs of features in sequences</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_union.xml --- a/emboss_union.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_union.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: union105" name="union" version="5.0.0"> +<tool id="EMBOSS: union105" name="union" version="@VERSION@"> <description>Reads sequence fragments and builds one sequence</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_vectorstrip.xml --- a/emboss_vectorstrip.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_vectorstrip.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="5.0.0.1"> +<tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="@VERSION@.1"> <description>Strips out DNA between a pair of vector sequences</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_water.xml --- a/emboss_water.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_water.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: water107" name="water" version="5.0.0.1"> +<tool id="EMBOSS: water107" name="water" version="@VERSION@.1"> <description>Smith-Waterman local alignment</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_wobble.xml --- a/emboss_wobble.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_wobble.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: wobble108" name="wobble" version="5.0.0.1"> +<tool id="EMBOSS: wobble108" name="wobble" version="@VERSION@.1"> <description>Wobble base plot</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_wordcount.xml --- a/emboss_wordcount.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_wordcount.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: wordcount109" name="wordcount" version="5.0.0.1"> +<tool id="EMBOSS: wordcount109" name="wordcount" version="@VERSION@.1"> <description>Counts words of a specified size in a DNA sequence</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f emboss_wordmatch.xml --- a/emboss_wordmatch.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/emboss_wordmatch.xml Fri Jun 22 03:24:47 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0.1"> +<tool id="EMBOSS: wordmatch110" name="wordmatch" version="@VERSION@.1"> <description>Finds all exact matches of a given size between 2 sequences</description> <macros> <import>macros.xml</import> |
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| diff -r 832c20329690 -r 8992d258e42f macros.xml --- a/macros.xml Mon Apr 23 13:05:09 2018 -0400 +++ b/macros.xml Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,7 +1,8 @@ <macros> + <token name="@VERSION@">5.0.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="5.0.0">emboss</requirement> + <requirement type="package" version="@VERSION@">emboss</requirement> </requirements> </xml> <xml name="citations"> |
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| diff -r 832c20329690 -r 8992d258e42f test-data/emboss_sixpack_out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_sixpack_out.fasta Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -0,0 +1,53 @@ +>Sequence_1_ORF1 Translation of Sequence in frame 1, ORF 1, threshold 1, 17aa +VRCLKYLLLSLHRPQFS +>Sequence_1_ORF2 Translation of Sequence in frame 1, ORF 2, threshold 1, 5aa +WLYTD +>Sequence_1_ORF3 Translation of Sequence in frame 1, ORF 3, threshold 1, 6aa +KFLCKH +>Sequence_1_ORF4 Translation of Sequence in frame 1, ORF 4, threshold 1, 12aa +LKAVGLECYRFV +>Sequence_1_ORF5 Translation of Sequence in frame 1, ORF 5, threshold 1, 33aa +LSASLALIKGSFSLLWKTLWKNTTSTSLSPLVC +>Sequence_1_ORF6 Translation of Sequence in frame 1, ORF 6, threshold 1, 25aa +LLDTVVIPFATPRNYLYELFSLYYM +>Sequence_1_ORF7 Translation of Sequence in frame 1, ORF 7, threshold 1, 3aa +VRL +>Sequence_1_ORF8 Translation of Sequence in frame 1, ORF 8, threshold 1, 40aa +SSFSKSFTVFDLNVHVLRLFWIICGQFNLRCFFLKYLFMV +>Sequence_1_ORF9 Translation of Sequence in frame 1, ORF 9, threshold 1, 29aa +FLVCTCSGASSLFTLFVYSSSFIFSMILI +>Sequence_2_ORF1 Translation of Sequence in frame 2, ORF 1, threshold 1, 3aa +FDA +>Sequence_2_ORF2 Translation of Sequence in frame 2, ORF 2, threshold 1, 27aa +NTFFCPYTDHSFPNGFTPTRNSCASTN +>Sequence_2_ORF3 Translation of Sequence in frame 2, ORF 3, threshold 1, 4aa +KRLA +>Sequence_2_ORF4 Translation of Sequence in frame 2, ORF 4, threshold 1, 7aa +SVTGLYS +>Sequence_2_ORF5 Translation of Sequence in frame 2, ORF 5, threshold 1, 5aa +ARLLP +>Sequence_2_ORF6 Translation of Sequence in frame 2, ORF 6, threshold 1, 32aa +SKVHFLYFGRRCGRIQQVRVSPPWFADYWIQL +>Sequence_2_ORF7 Translation of Sequence in frame 2, ORF 7, threshold 1, 46aa +YPSQHRVTIYMNYFPFIICSRFVFNLPLASLLLFSTSMFMFLGCFG +>Sequence_2_ORF8 Translation of Sequence in frame 2, ORF 8, threshold 1, 11aa +YAVSLIFVVSS +>Sequence_2_ORF9 Translation of Sequence in frame 2, ORF 9, threshold 1, 32aa +NIYSWFNFWFVLVQGPVHYLLCLYTAVLLFLV +>Sequence_2_ORF10 Translation of Sequence in frame 2, ORF 10, threshold 1, 1aa +F +>Sequence_3_ORF1 Translation of Sequence in frame 3, ORF 1, threshold 1, 90aa +SMPKIPSFVPTQTTVFLMALHRLEILVQALIESGWPRVLPVCIAERVSCPDQRFIFSTLE +DVVEEYNKYESLPPGLLITGYSCNTLRNTA +>Sequence_3_ORF2 Translation of Sequence in frame 3, ORF 2, threshold 1, 3aa +LSI +>Sequence_3_ORF3 Translation of Sequence in frame 3, ORF 3, threshold 1, 16aa +IIFPLLYVVGSSLIFL +>Sequence_3_ORF4 Translation of Sequence in frame 3, ORF 4, threshold 1, 13aa +QVFYCFRPQCSCS +>Sequence_3_ORF5 Translation of Sequence in frame 3, ORF 5, threshold 1, 9aa +VVLDNMRSV +>Sequence_3_ORF6 Translation of Sequence in frame 3, ORF 6, threshold 1, 37aa +SSLFLLKIFIHGLIFGLYLFRGQFIIYSVCIQQFFYF +>Sequence_3_ORF7 Translation of Sequence in frame 3, ORF 7, threshold 1, 8aa +YDFNLKQF |
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| diff -r 832c20329690 -r 8992d258e42f test-data/emboss_sixpack_out2.sixpack --- a/test-data/emboss_sixpack_out2.sixpack Mon Apr 23 13:05:09 2018 -0400 +++ b/test-data/emboss_sixpack_out2.sixpack Fri Jun 22 03:24:47 2018 -0400 |
| b |
| @@ -1,4 +1,3 @@ - V R C L K Y L L L S L H R P Q F S * W L F1 F D A * N T F F C P Y T D H S F P N G F F2 @@ -6,11 +5,6 @@ gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----| - caagctacggattttatggaagaaaacagggatgtgtctggtgtcaaaaggattaccgaa - T R H R F Y R R K D R C L G C N E * H S F6 - X E I G L I G E K T G V C V V T K R I A F5 - N S A * F V K K Q G * V S W L K G L P K F4 - Y T D * K F L C K H * L K A V G L E C Y F1 T P T R N S C A S T N * K R L A * S V T F2 @@ -18,11 +12,6 @@ tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac 70 80 90 100 110 120 ----:----|----:----|----:----|----:----|----:----|----:----| - atgtggctgatctttaagaacacgttcgtgattaactttcgccaaccggatctcacaatg - * V S * F N K H L C * N F A T P R S H * F6 - K C R S S I R T C A S I S L P Q G L T N F5 - V G V L F E Q A L V L Q F R N A * L T V F4 - R F V * L S A S L A L I K G S F S L L W F1 G L Y S * A R L L P * S K V H F L Y F G F2 @@ -30,11 +19,6 @@ cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg 130 140 150 160 170 180 ----:----|----:----|----:----|----:----|----:----|----:----| - gccaaacatatcgactcgcgcagagaacgggactagtttccaagtaaaagagatgaaacc - R N T Y S L A D R A R I L P E N E R S Q F6 - G T Q I A S R T E Q G S * L N M K E V K F5 - P K Y L Q A R R K G Q D F T * K R * K P F4 - K T L W K N T T S T S L S P L V C * L L F1 R R C G R I Q Q V R V S P P W F A D Y W F2 @@ -42,11 +26,6 @@ aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg 190 200 210 220 230 240 ----:----|----:----|----:----|----:----|----:----|----:----| - ttctgcaacaccttcttatgttgttcatgctcagagaggggggaccaaacgactaatgac - F V N H F F V V L V L R E G R T Q Q N S F6 - S S T T S S Y L L Y S D R G G P K S I V F5 - L R Q P L I C C T R T E G G Q N A S * Q F4 - D T V V I P F A T P R N Y L Y E L F S L F1 I Q L * Y P S Q H R V T I Y M N Y F P F F2 @@ -54,11 +33,6 @@ gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt 250 260 270 280 290 300 ----:----|----:----|----:----|----:----|----:----|----:----| - ctatgtcaacattatgggaagcgttgtggcgcattgatagatatacttaataaaagggaa - S V T T I G K A V G R L * R Y S N N E R F6 - P Y L Q L V R R L V A Y S D I H I I K G F5 - I C N Y Y G E C C R T V I * I F * K G K F4 - Y Y M * * V R L * S S F S K S F T V F D F1 I I C S R F V F N L P L A S L L L F S T F2 @@ -66,11 +40,6 @@ tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac 310 320 330 340 350 360 ----:----|----:----|----:----|----:----|----:----|----:----| - ataatatacatcatccaagcagaaattagaaggaaatcgttcagaaaatgacaaaagctg - * * I Y Y T R R * D E K L L D K V T K S F6 - K N Y T T P E D K I K R * C T K * Q K R F5 - I I H L L N T K L R G K A L R K S N E V F4 - L N V H V L R L F W I I C G Q F N L R C F1 S M F M F L G C F G * Y A V S L I F V V F2 @@ -78,11 +47,6 @@ ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt 370 380 390 400 410 420 ----:----|----:----|----:----|----:----|----:----|----:----| - gagttacaagtacaagaatccaacaaaacctattatacgccagtcaaattagaagcaaca - R L T * T R L N N Q I I H P * N L R R Q F6 - G * H E H E * T T K S L I R D T * D E N F5 - E I N M N K P Q K P Y Y A T L K I K T T F4 - F F L K Y L F M V * F L V C T C S G A S F1 S S * N I Y S W F N F W F V L V Q G P V F2 @@ -90,11 +54,6 @@ ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt 430 440 450 460 470 480 ----:----|----:----|----:----|----:----|----:----|----:----| - aagaagaattttataaataagtaccaaattaaaaaccaaacatgaacaagtccccggtca - K K K F Y K N M T * N K T Q V Q E P A L F6 - N R R L I N I * P K I K P K Y K N L P W F5 - E E * F I * E H N L K Q N T S T * P G T F4 - S L F T L F V Y S S S F I F S M I L I * F1 H Y L L C L Y T A V L L F L V * F * F K F2 @@ -102,11 +61,6 @@ tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa 490 500 510 520 530 540 ----:----|----:----|----:----|----:----|----:----|----:----| - agtaataaatgagacaaacatatgtcgtcaagaaaataaaaatcatactaaaattaaatt - E N N V R N T Y L L E K I K L I I K I * F6 - N M I * E T Q I C C N K * K * Y S K L K F5 - * * K S Q K Y V A T R K N K T H N * N L F4 - N N S N G Q K F1 T I L M V K X F2 @@ -114,21 +68,14 @@ aacaattctaatggtcaaaaa 550 560 ----:----|----:----|- - ttgttaagattaccagttttt - F L E L P * F F6 - F C N * H D F F5 - V I R I T L F F4 ############################## Minimum size of ORFs : 1 -Total ORFs in frame 1 : 10 -Total ORFs in frame 2 : 11 -Total ORFs in frame 3 : 8 -Total ORFs in frame 4 : 14 -Total ORFs in frame 5 : 12 -Total ORFs in frame 6 : 14 +Total ORFs in frame 1 : 9 +Total ORFs in frame 2 : 10 +Total ORFs in frame 3 : 7 -Total ORFs : 69 +Total ORFs : 26 ############################## |