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changeset 13:8992d258e42f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
author iuc
date Fri, 22 Jun 2018 03:24:47 -0400
parents 832c20329690
children 2e0fb4bc860e
files 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_out.fasta test-data/emboss_sixpack_out2.sixpack
diffstat 109 files changed, 175 insertions(+), 169 deletions(-) [+]
line wrap: on
line diff
--- a/emboss_antigenic.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_antigenic.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_backtranseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_backtranseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_banana.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_banana.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_biosed.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_biosed.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_btwisted.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_btwisted.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_cai.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_cai.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- 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
@@ -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>
--- a/emboss_chaos.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_chaos.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_charge.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_charge.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_checktrans.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_checktrans.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_chips.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_chips.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_cirdna.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_cirdna.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_codcmp.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_codcmp.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_coderet.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_coderet.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_compseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_compseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_cpgplot.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_cpgplot.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_cpgreport.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_cpgreport.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_cusp.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_cusp.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_cutseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_cutseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_dan.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_dan.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_degapseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_degapseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_descseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_descseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_diffseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_diffseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_digest.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_digest.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_dotmatcher.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_dotmatcher.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_dotpath.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_dotpath.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_dottup.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_dottup.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_dreg.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_dreg.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_einverted.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_einverted.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_epestfind.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_epestfind.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_equicktandem.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_equicktandem.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_est2genome.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_est2genome.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_etandem.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_etandem.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_extractfeat.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_extractfeat.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_extractseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_extractseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_freak.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_freak.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_fuzzpro.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_fuzzpro.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_fuzztran.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_fuzztran.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_garnier.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_garnier.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_geecee.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_geecee.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_getorf.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_getorf.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_helixturnhelix.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_helixturnhelix.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_hmoment.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_hmoment.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_iep.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_iep.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_infoseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_infoseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_isochore.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_isochore.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_lindna.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_lindna.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_marscan.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_marscan.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_maskfeat.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_maskfeat.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_maskseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_maskseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_matcher.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_matcher.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_megamerger.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_megamerger.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_merger.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_merger.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_msbar.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_msbar.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_needle.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_needle.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_newcpgreport.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_newcpgreport.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_newcpgseek.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_newcpgseek.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_newseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_newseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_noreturn.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_noreturn.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_notseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_notseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_nthseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_nthseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_octanol.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_octanol.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_oddcomp.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_oddcomp.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_palindrome.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_palindrome.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_pasteseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_pasteseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_patmatdb.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_patmatdb.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_pepcoil.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_pepcoil.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_pepinfo.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_pepinfo.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_pepnet.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_pepnet.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_pepstats.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_pepstats.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_pepwheel.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_pepwheel.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_pepwindow.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_pepwindow.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_pepwindowall.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_pepwindowall.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_plotcon.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_plotcon.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_plotorf.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_plotorf.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_polydot.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_polydot.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_preg.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_preg.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_prettyplot.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_prettyplot.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_prettyseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_prettyseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_primersearch.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_primersearch.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_revseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_revseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_seqmatchall.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_seqmatchall.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_seqret.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_seqret.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_showfeat.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_showfeat.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_shuffleseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_shuffleseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_sigcleave.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_sigcleave.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_sirna.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_sirna.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- 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
 
--- a/emboss_skipseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_skipseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_splitter.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_splitter.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_supermatcher.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_supermatcher.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_syco.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_syco.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_tcode.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_tcode.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_textsearch.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_textsearch.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_tmap.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_tmap.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_tranalign.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_tranalign.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_transeq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_transeq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_trimest.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_trimest.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_trimseq.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_trimseq.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_twofeat.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_twofeat.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_union.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_union.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_vectorstrip.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_vectorstrip.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_water.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_water.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_wobble.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_wobble.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_wordcount.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_wordcount.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/emboss_wordmatch.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/emboss_wordmatch.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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>
--- a/macros.xml	Mon Apr 23 13:05:09 2018 -0400
+++ b/macros.xml	Fri Jun 22 03:24:47 2018 -0400
@@ -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">
--- /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
@@ -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
--- 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
@@ -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
 ##############################