From e05f11bc735442a52c78a6577d863d5c0a03bb72 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 7 Oct 2010 16:23:57 -0400
Subject: [PATCH] Convert a bunch of binary requirement tags to package
 requirements, and change the sputnik tool to call 'sputnik' instead of
 'bx-sputnik'.

---
 tools/emboss_5/emboss_antigenic.xml                    | 1 +
 tools/emboss_5/emboss_backtranseq.xml                  | 1 +
 tools/emboss_5/emboss_banana.xml                       | 1 +
 tools/emboss_5/emboss_biosed.xml                       | 1 +
 tools/emboss_5/emboss_btwisted.xml                     | 1 +
 tools/emboss_5/emboss_cai.xml                          | 1 +
 tools/emboss_5/emboss_cai_custom.xml                   | 1 +
 tools/emboss_5/emboss_chaos.xml                        | 1 +
 tools/emboss_5/emboss_charge.xml                       | 1 +
 tools/emboss_5/emboss_checktrans.xml                   | 1 +
 tools/emboss_5/emboss_chips.xml                        | 1 +
 tools/emboss_5/emboss_cirdna.xml                       | 1 +
 tools/emboss_5/emboss_codcmp.xml                       | 1 +
 tools/emboss_5/emboss_coderet.xml                      | 1 +
 tools/emboss_5/emboss_compseq.xml                      | 1 +
 tools/emboss_5/emboss_cpgplot.xml                      | 1 +
 tools/emboss_5/emboss_cpgreport.xml                    | 1 +
 tools/emboss_5/emboss_cusp.xml                         | 1 +
 tools/emboss_5/emboss_cutseq.xml                       | 1 +
 tools/emboss_5/emboss_dan.xml                          | 1 +
 tools/emboss_5/emboss_degapseq.xml                     | 1 +
 tools/emboss_5/emboss_descseq.xml                      | 1 +
 tools/emboss_5/emboss_diffseq.xml                      | 1 +
 tools/emboss_5/emboss_digest.xml                       | 1 +
 tools/emboss_5/emboss_dotmatcher.xml                   | 1 +
 tools/emboss_5/emboss_dotpath.xml                      | 1 +
 tools/emboss_5/emboss_dottup.xml                       | 1 +
 tools/emboss_5/emboss_dreg.xml                         | 1 +
 tools/emboss_5/emboss_einverted.xml                    | 1 +
 tools/emboss_5/emboss_epestfind.xml                    | 1 +
 tools/emboss_5/emboss_equicktandem.xml                 | 1 +
 tools/emboss_5/emboss_est2genome.xml                   | 1 +
 tools/emboss_5/emboss_etandem.xml                      | 1 +
 tools/emboss_5/emboss_extractfeat.xml                  | 1 +
 tools/emboss_5/emboss_extractseq.xml                   | 1 +
 tools/emboss_5/emboss_freak.xml                        | 1 +
 tools/emboss_5/emboss_fuzznuc.xml                      | 1 +
 tools/emboss_5/emboss_fuzzpro.xml                      | 1 +
 tools/emboss_5/emboss_fuzztran.xml                     | 1 +
 tools/emboss_5/emboss_garnier.xml                      | 1 +
 tools/emboss_5/emboss_geecee.xml                       | 1 +
 tools/emboss_5/emboss_getorf.xml                       | 1 +
 tools/emboss_5/emboss_helixturnhelix.xml               | 1 +
 tools/emboss_5/emboss_hmoment.xml                      | 1 +
 tools/emboss_5/emboss_iep.xml                          | 1 +
 tools/emboss_5/emboss_infoseq.xml                      | 1 +
 tools/emboss_5/emboss_isochore.xml                     | 1 +
 tools/emboss_5/emboss_lindna.xml                       | 1 +
 tools/emboss_5/emboss_marscan.xml                      | 1 +
 tools/emboss_5/emboss_maskfeat.xml                     | 1 +
 tools/emboss_5/emboss_maskseq.xml                      | 1 +
 tools/emboss_5/emboss_matcher.xml                      | 1 +
 tools/emboss_5/emboss_megamerger.xml                   | 1 +
 tools/emboss_5/emboss_merger.xml                       | 1 +
 tools/emboss_5/emboss_msbar.xml                        | 1 +
 tools/emboss_5/emboss_needle.xml                       | 1 +
 tools/emboss_5/emboss_newcpgreport.xml                 | 1 +
 tools/emboss_5/emboss_newcpgseek.xml                   | 1 +
 tools/emboss_5/emboss_newseq.xml                       | 1 +
 tools/emboss_5/emboss_noreturn.xml                     | 1 +
 tools/emboss_5/emboss_notseq.xml                       | 1 +
 tools/emboss_5/emboss_nthseq.xml                       | 1 +
 tools/emboss_5/emboss_octanol.xml                      | 1 +
 tools/emboss_5/emboss_oddcomp.xml                      | 1 +
 tools/emboss_5/emboss_palindrome.xml                   | 1 +
 tools/emboss_5/emboss_pasteseq.xml                     | 1 +
 tools/emboss_5/emboss_patmatdb.xml                     | 1 +
 tools/emboss_5/emboss_pepcoil.xml                      | 1 +
 tools/emboss_5/emboss_pepinfo.xml                      | 1 +
 tools/emboss_5/emboss_pepnet.xml                       | 1 +
 tools/emboss_5/emboss_pepstats.xml                     | 1 +
 tools/emboss_5/emboss_pepwheel.xml                     | 1 +
 tools/emboss_5/emboss_pepwindow.xml                    | 1 +
 tools/emboss_5/emboss_pepwindowall.xml                 | 1 +
 tools/emboss_5/emboss_plotcon.xml                      | 1 +
 tools/emboss_5/emboss_plotorf.xml                      | 1 +
 tools/emboss_5/emboss_polydot.xml                      | 1 +
 tools/emboss_5/emboss_preg.xml                         | 1 +
 tools/emboss_5/emboss_prettyplot.xml                   | 1 +
 tools/emboss_5/emboss_prettyseq.xml                    | 1 +
 tools/emboss_5/emboss_primersearch.xml                 | 1 +
 tools/emboss_5/emboss_revseq.xml                       | 1 +
 tools/emboss_5/emboss_seqmatchall.xml                  | 1 +
 tools/emboss_5/emboss_seqret.xml                       | 1 +
 tools/emboss_5/emboss_showfeat.xml                     | 1 +
 tools/emboss_5/emboss_shuffleseq.xml                   | 1 +
 tools/emboss_5/emboss_sigcleave.xml                    | 1 +
 tools/emboss_5/emboss_sirna.xml                        | 1 +
 tools/emboss_5/emboss_sixpack.xml                      | 1 +
 tools/emboss_5/emboss_skipseq.xml                      | 1 +
 tools/emboss_5/emboss_splitter.xml                     | 1 +
 tools/emboss_5/emboss_supermatcher.xml                 | 1 +
 tools/emboss_5/emboss_syco.xml                         | 1 +
 tools/emboss_5/emboss_tcode.xml                        | 1 +
 tools/emboss_5/emboss_textsearch.xml                   | 1 +
 tools/emboss_5/emboss_tmap.xml                         | 1 +
 tools/emboss_5/emboss_tranalign.xml                    | 1 +
 tools/emboss_5/emboss_transeq.xml                      | 1 +
 tools/emboss_5/emboss_trimest.xml                      | 1 +
 tools/emboss_5/emboss_trimseq.xml                      | 1 +
 tools/emboss_5/emboss_twofeat.xml                      | 1 +
 tools/emboss_5/emboss_union.xml                        | 1 +
 tools/emboss_5/emboss_vectorstrip.xml                  | 1 +
 tools/emboss_5/emboss_water.xml                        | 1 +
 tools/emboss_5/emboss_wobble.xml                       | 1 +
 tools/emboss_5/emboss_wordcount.xml                    | 1 +
 tools/emboss_5/emboss_wordmatch.xml                    | 1 +
 tools/evolution/add_scores.xml                         | 2 +-
 tools/evolution/codingSnps.xml                         | 2 +-
 tools/extract/liftOver_wrapper.xml                     | 2 +-
 tools/fastx_toolkit/fasta_clipping_histogram.xml       | 1 +
 tools/fastx_toolkit/fasta_formatter.xml                | 1 +
 tools/fastx_toolkit/fasta_nucleotide_changer.xml       | 1 +
 tools/fastx_toolkit/fastq_quality_boxplot.xml          | 1 +
 tools/fastx_toolkit/fastq_quality_converter.xml        | 1 +
 tools/fastx_toolkit/fastq_quality_filter.xml           | 1 +
 tools/fastx_toolkit/fastq_to_fasta.xml                 | 1 +
 tools/fastx_toolkit/fastx_artifacts_filter.xml         | 1 +
 tools/fastx_toolkit/fastx_barcode_splitter.xml         | 1 +
 tools/fastx_toolkit/fastx_clipper.xml                  | 1 +
 tools/fastx_toolkit/fastx_collapser.xml                | 1 +
 tools/fastx_toolkit/fastx_nucleotides_distribution.xml | 1 +
 tools/fastx_toolkit/fastx_quality_statistics.xml       | 1 +
 tools/fastx_toolkit/fastx_renamer.xml                  | 1 +
 tools/fastx_toolkit/fastx_reverse_complement.xml       | 1 +
 tools/fastx_toolkit/fastx_trimmer.xml                  | 1 +
 tools/filters/wig_to_bigwig.xml                        | 2 +-
 tools/metag_tools/megablast_wrapper.xml                | 2 +-
 tools/ngs_rna/cuffcompare_wrapper.xml                  | 3 +++
 tools/ngs_rna/cuffdiff_wrapper.xml                     | 3 +++
 tools/ngs_rna/cufflinks_wrapper.xml                    | 3 +++
 tools/ngs_rna/tophat_wrapper.xml                       | 3 +++
 tools/peak_calling/macs_wrapper.xml                    | 1 -
 tools/regVariation/microsats_alignment_level.xml       | 4 ++--
 tools/sr_assembly/velvetg.xml                          | 2 +-
 tools/sr_assembly/velveth.xml                          | 2 +-
 tools/sr_mapping/PerM.xml                              | 3 +++
 tools/sr_mapping/bfast_wrapper.xml                     | 2 +-
 tools/sr_mapping/bowtie_color_wrapper.xml              | 1 +
 tools/sr_mapping/lastz_paired_reads_wrapper.xml        | 2 +-
 tools/sr_mapping/lastz_wrapper.xml                     | 2 +-
 tools/taxonomy/find_diag_hits.xml                      | 3 +++
 tools/taxonomy/gi2taxonomy.xml                         | 3 +++
 tools/taxonomy/lca.xml                                 | 5 ++++-
 tools/taxonomy/poisson2test.xml                        | 3 +++
 tools/taxonomy/t2ps_wrapper.xml                        | 3 +++
 tools/taxonomy/t2t_report.xml                          | 3 +++
 147 files changed, 170 insertions(+), 14 deletions(-)

diff --git a/tools/emboss_5/emboss_antigenic.xml b/tools/emboss_5/emboss_antigenic.xml
index 52eff617956..523e07759b1 100644
--- a/tools/emboss_5/emboss_antigenic.xml
+++ b/tools/emboss_5/emboss_antigenic.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: antigenic1" name="antigenic" version="5.0.0">
   <description>Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>antigenic -sequence $input1 -outfile $out_file1 -minlen $minlen -rformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_backtranseq.xml b/tools/emboss_5/emboss_backtranseq.xml
index efa6f42c542..02dd25eeb70 100644
--- a/tools/emboss_5/emboss_backtranseq.xml
+++ b/tools/emboss_5/emboss_backtranseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: backtranseq2" name="backtranseq" version="5.0.0">
   <description>Back translate a protein sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>backtranseq -sequence $input1 -outfile $out_file1 -cfile $cfile -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_banana.xml b/tools/emboss_5/emboss_banana.xml
index 778dff8a2b8..720de4720a0 100644
--- a/tools/emboss_5/emboss_banana.xml
+++ b/tools/emboss_5/emboss_banana.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: banana3" name="banana" version="5.0.0">
   <description>Bending and curvature plot in B-DNA</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>banana -sequence $input1 -outfile $out_file1 -graph none -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_biosed.xml b/tools/emboss_5/emboss_biosed.xml
index 6875dc775e4..961ee9c06bd 100644
--- a/tools/emboss_5/emboss_biosed.xml
+++ b/tools/emboss_5/emboss_biosed.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: biosed4" name="biosed" version="5.0.0">
   <description>Replace or delete sequence sections</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>biosed -sequence $input1 -outseq $out_file1 -target $target -replace $replace -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_btwisted.xml b/tools/emboss_5/emboss_btwisted.xml
index 097f5eca5e4..edf4efadfbe 100644
--- a/tools/emboss_5/emboss_btwisted.xml
+++ b/tools/emboss_5/emboss_btwisted.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: btwisted5" name="btwisted" version="5.0.0">
   <description>Calculates the twisting in a B-DNA sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>btwisted -sequence $input1 -outfile $out_file1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_cai.xml b/tools/emboss_5/emboss_cai.xml
index 3170d708d6e..5d6621271ac 100644
--- a/tools/emboss_5/emboss_cai.xml
+++ b/tools/emboss_5/emboss_cai.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: cai6" name="cai" version="5.0.0">
   <description>CAI codon adaptation index</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>cai -seqall $input1 -outfile $out_file1 -cfile $cfile -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_cai_custom.xml b/tools/emboss_5/emboss_cai_custom.xml
index b5e15582694..29992a5cf24 100644
--- a/tools/emboss_5/emboss_cai_custom.xml
+++ b/tools/emboss_5/emboss_cai_custom.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: cai_custom6" name="cai custom" version="5.0.0">
   <description>CAI codon adaptation index using custom codon usage file</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>cai -seqall $input1 -outfile $out_file1 -cfile $input2 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_chaos.xml b/tools/emboss_5/emboss_chaos.xml
index b59bc645f4c..71c88ae16d0 100644
--- a/tools/emboss_5/emboss_chaos.xml
+++ b/tools/emboss_5/emboss_chaos.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: chaos7" name="chaos" version="5.0.0">
   <description>Create a chaos game representation plot for a sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl chaos -sequence $input1 -graph png -goutfile $out_file1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_charge.xml b/tools/emboss_5/emboss_charge.xml
index 8d6d5b9eded..91976dc479c 100644
--- a/tools/emboss_5/emboss_charge.xml
+++ b/tools/emboss_5/emboss_charge.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: charge8" name="charge" version="5.0.0">
   <description>Protein charge plot</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>charge -seqall $input1 -outfile $out_file1 -window $window -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_checktrans.xml b/tools/emboss_5/emboss_checktrans.xml
index 22d0ee752ad..5dbe5a8c66c 100644
--- a/tools/emboss_5/emboss_checktrans.xml
+++ b/tools/emboss_5/emboss_checktrans.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0">
   <description>Reports STOP codons and ORF statistics of a protein</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>checktrans -sequence $input1 -outfile $out_file1 -outseq $out_file2 -osformat3 $out_format2 -outfeat $out_file3 -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_chips.xml b/tools/emboss_5/emboss_chips.xml
index 6302d84f29c..cc054b02b1c 100644
--- a/tools/emboss_5/emboss_chips.xml
+++ b/tools/emboss_5/emboss_chips.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: chips10" name="chips" version="5.0.0">
   <description>Codon usage statistics</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>chips -seqall $input1 -outfile $out_file1 -sum $sum -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_cirdna.xml b/tools/emboss_5/emboss_cirdna.xml
index bec2fcae21a..fe69619a17d 100644
--- a/tools/emboss_5/emboss_cirdna.xml
+++ b/tools/emboss_5/emboss_cirdna.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: cirdna11" name="cirdna" version="5.0.0">
   <description>Draws circular maps of DNA constructs</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl cirdna -infile $input1 -graphout png -goutfile $out_file1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_codcmp.xml b/tools/emboss_5/emboss_codcmp.xml
index 204aa5407ca..f720515a843 100644
--- a/tools/emboss_5/emboss_codcmp.xml
+++ b/tools/emboss_5/emboss_codcmp.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: codcmp12" name="codcmp" version="5.0.0">
   <description>Codon usage table comparison</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>codcmp -first $cfile1 -second $cfile2 -outfile $out_file1 -auto</command>
   <inputs>
     <param name="cfile1" type="select">
diff --git a/tools/emboss_5/emboss_coderet.xml b/tools/emboss_5/emboss_coderet.xml
index fe2ba6ceaea..d19bb0e8ea5 100644
--- a/tools/emboss_5/emboss_coderet.xml
+++ b/tools/emboss_5/emboss_coderet.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: coderet13" name="coderet" version="5.0.0">
   <description>Extract CDS, mRNA and translations from feature tables</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <!--  <command>coderet -seqall $input1 -outfile $out_file1 -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>-->
   <command>coderet -seqall $input1 -outfile $out_file1 -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_compseq.xml b/tools/emboss_5/emboss_compseq.xml
index 924675a32a7..55a79f723d3 100644
--- a/tools/emboss_5/emboss_compseq.xml
+++ b/tools/emboss_5/emboss_compseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: compseq14" name="compseq" version="5.0.0">
   <description>Count composition of dimer/trimer/etc words in a sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_cpgplot.xml b/tools/emboss_5/emboss_cpgplot.xml
index 6fc370862ce..72bd3159206 100644
--- a/tools/emboss_5/emboss_cpgplot.xml
+++ b/tools/emboss_5/emboss_cpgplot.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0">
   <description>Plot CpG rich areas</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence $input1 -window $window -minlen $minlen -minpc $minpc -outfile $outfile -graph png -goutfile $goutfile -outfeat $outfeat -minoe $minoe -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_cpgreport.xml b/tools/emboss_5/emboss_cpgreport.xml
index ee74d22df8f..c6b5dc70490 100644
--- a/tools/emboss_5/emboss_cpgreport.xml
+++ b/tools/emboss_5/emboss_cpgreport.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0">
   <description>Reports all CpG rich regions</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>cpgreport -sequence $input1 -outfile $out_file1 -outfeat $out_file2 -offormat3 $out_format2 -score $score -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_cusp.xml b/tools/emboss_5/emboss_cusp.xml
index 049bba64106..9db95968271 100644
--- a/tools/emboss_5/emboss_cusp.xml
+++ b/tools/emboss_5/emboss_cusp.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: cusp17" name="cusp" version="5.0.0">
   <description>Create a codon usage table</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>cusp -sequence $input1 -outfile $out_file1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_cutseq.xml b/tools/emboss_5/emboss_cutseq.xml
index c4582190aad..044efafee6c 100644
--- a/tools/emboss_5/emboss_cutseq.xml
+++ b/tools/emboss_5/emboss_cutseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: cutseq18" name="cutseq" version="5.0.0">
   <description>Removes a specified section from a sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>cutseq -sequence $input1 -outseq $out_file1 -from $from -to $to -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_dan.xml b/tools/emboss_5/emboss_dan.xml
index d333935bd0e..8a590421b94 100644
--- a/tools/emboss_5/emboss_dan.xml
+++ b/tools/emboss_5/emboss_dan.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: dan19" name="dan" version="5.0.0">
   <description>Calculates DNA RNA/DNA melting temperature</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc
   -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_degapseq.xml b/tools/emboss_5/emboss_degapseq.xml
index cdf0a074bdc..cf2a0394c10 100644
--- a/tools/emboss_5/emboss_degapseq.xml
+++ b/tools/emboss_5/emboss_degapseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: degapseq20" name="degapseq" version="5.0.0">
   <description>Removes gap characters from sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>degapseq -sequence $input1 -outseq $out_file1 -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_descseq.xml b/tools/emboss_5/emboss_descseq.xml
index 1a0bc9c9033..ba1d193dd70 100644
--- a/tools/emboss_5/emboss_descseq.xml
+++ b/tools/emboss_5/emboss_descseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: descseq21" name="descseq" version="5.0.0">
   <description>Alter the name or description of a sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>descseq -sequence $input1 -outseq $out_file1 -name "$seqname" -description "$desc" -append $append -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_diffseq.xml b/tools/emboss_5/emboss_diffseq.xml
index caac9445641..88c08052d40 100644
--- a/tools/emboss_5/emboss_diffseq.xml
+++ b/tools/emboss_5/emboss_diffseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0">
   <description>Find differences between nearly identical sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3
   $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_digest.xml b/tools/emboss_5/emboss_digest.xml
index 0630a37bff4..a6260e24a79 100644
--- a/tools/emboss_5/emboss_digest.xml
+++ b/tools/emboss_5/emboss_digest.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: digest23" name="digest" version="5.0.0">
   <description>Protein proteolytic enzyme or reagent cleavage digest</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>digest -seqall $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_dotmatcher.xml b/tools/emboss_5/emboss_dotmatcher.xml
index cdfecdd2856..99f4c7f2d59 100644
--- a/tools/emboss_5/emboss_dotmatcher.xml
+++ b/tools/emboss_5/emboss_dotmatcher.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: dotmatcher24" name="dotmatcher" version="5.0.0">
   <description>Displays a thresholded dotplot of two sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotmatcher -asequence $input1 -bsequence $input2 -goutfile $out_file1 -windowsize $windowsize -threshold $threshold -graph png -xygraph png
   -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_dotpath.xml b/tools/emboss_5/emboss_dotpath.xml
index 9716a1b9061..b0cffc62ae8 100644
--- a/tools/emboss_5/emboss_dotpath.xml
+++ b/tools/emboss_5/emboss_dotpath.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: dotpath25" name="dotpath" version="5.0.0">
   <description>Non-overlapping wordmatch dotplot of two sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotpath -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png
   -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_dottup.xml b/tools/emboss_5/emboss_dottup.xml
index d3f9e05c1ce..9ee146a0dd8 100644
--- a/tools/emboss_5/emboss_dottup.xml
+++ b/tools/emboss_5/emboss_dottup.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: dottup26" name="dottup" version="5.0.0">
   <description>Displays a wordmatch dotplot of two sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl dottup -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -boxit $boxit -graph png  -xygraph png -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_dreg.xml b/tools/emboss_5/emboss_dreg.xml
index f51de0423a7..25725d49be6 100644
--- a/tools/emboss_5/emboss_dreg.xml
+++ b/tools/emboss_5/emboss_dreg.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: dreg27" name="dreg" version="5.0.0">
   <description>Regular expression search of a nucleotide sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>dreg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_einverted.xml b/tools/emboss_5/emboss_einverted.xml
index 6b82d99e49e..90772546bc5 100644
--- a/tools/emboss_5/emboss_einverted.xml
+++ b/tools/emboss_5/emboss_einverted.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: einverted28" name="einverted" version="5.0.0">
   <description>Finds DNA inverted repeats</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_epestfind.xml b/tools/emboss_5/emboss_epestfind.xml
index b96efe25c0e..8cfb938b23c 100644
--- a/tools/emboss_5/emboss_epestfind.xml
+++ b/tools/emboss_5/emboss_epestfind.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0">
   <description>Finds PEST motifs as potential proteolytic cleavage sites</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor
   -invalid $invalid -map $map -graph png -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_equicktandem.xml b/tools/emboss_5/emboss_equicktandem.xml
index 4ab5172f73a..a881ae3c8bf 100644
--- a/tools/emboss_5/emboss_equicktandem.xml
+++ b/tools/emboss_5/emboss_equicktandem.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: equicktandem31" name="equicktandem" version="5.0.0">
   <description>Finds tandem repeats</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_est2genome.xml b/tools/emboss_5/emboss_est2genome.xml
index f2b49f632d0..9bc7ed0c5e1 100644
--- a/tools/emboss_5/emboss_est2genome.xml
+++ b/tools/emboss_5/emboss_est2genome.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0">
   <description>Align EST and genomic DNA sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty
   $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_etandem.xml b/tools/emboss_5/emboss_etandem.xml
index 7165230c562..66e8be86b56 100644
--- a/tools/emboss_5/emboss_etandem.xml
+++ b/tools/emboss_5/emboss_etandem.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: etandem33" name="etandem" version="5.0.0">
   <description>Looks for tandem repeats in a nucleotide sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>etandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_extractfeat.xml b/tools/emboss_5/emboss_extractfeat.xml
index e13b4af1dc8..9759ce9dab1 100644
--- a/tools/emboss_5/emboss_extractfeat.xml
+++ b/tools/emboss_5/emboss_extractfeat.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: extractfeat34" name="extractfeat" version="5.0.0">
   <!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences -->  
   <description>Extract features from a sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>extractfeat -sequence $input1 -outseq $out_file1 -before $before -after $after -source "$source" -type "$type" -sense $sense -minscore $minscore -maxscore $maxscore -tag "$tag" -value
   "$value" -join $join -featinname $featinname -describe "$describe" -osformat2 $out_format1 -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_extractseq.xml b/tools/emboss_5/emboss_extractseq.xml
index 195cab20fae..f914654dc75 100644
--- a/tools/emboss_5/emboss_extractseq.xml
+++ b/tools/emboss_5/emboss_extractseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: extractseq35" name="extractseq" version="5.0.0">
   <description>Extract regions from a sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>extractseq -sequence $input1 -outseq $out_file1 -regions $regions -separate $separate -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_freak.xml b/tools/emboss_5/emboss_freak.xml
index 4547a80a3b9..ea1b969ebbb 100644
--- a/tools/emboss_5/emboss_freak.xml
+++ b/tools/emboss_5/emboss_freak.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: freak36" name="freak" version="5.0.0">
   <description>Residue/base frequency table or plot</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>freak -seqall $input1 -outfile $out_file1 -window $window -letters $letters -graph png -step $step -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_fuzznuc.xml b/tools/emboss_5/emboss_fuzznuc.xml
index 31cdadfe583..91b848fc31c 100644
--- a/tools/emboss_5/emboss_fuzznuc.xml
+++ b/tools/emboss_5/emboss_fuzznuc.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.1">
   <description>Nucleic acid pattern search</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_fuzzpro.xml b/tools/emboss_5/emboss_fuzzpro.xml
index f893fad8302..5de84234fb7 100644
--- a/tools/emboss_5/emboss_fuzzpro.xml
+++ b/tools/emboss_5/emboss_fuzzpro.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: fuzzpro38" name="fuzzpro" version="5.0.0">
   <description>Protein pattern search</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>fuzzpro -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -rformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_fuzztran.xml b/tools/emboss_5/emboss_fuzztran.xml
index 05ccdbcfe75..33056748a3a 100644
--- a/tools/emboss_5/emboss_fuzztran.xml
+++ b/tools/emboss_5/emboss_fuzztran.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0">
   <description>Protein pattern search after translation</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_garnier.xml b/tools/emboss_5/emboss_garnier.xml
index c2bb6a9441c..aab314a84ca 100644
--- a/tools/emboss_5/emboss_garnier.xml
+++ b/tools/emboss_5/emboss_garnier.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: garnier40" name="garnier" version="5.0.0">
   <description>Predicts protein secondary structure</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>garnier -sequence $input1 -outfile $out_file1 -idc $idc -rformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_geecee.xml b/tools/emboss_5/emboss_geecee.xml
index d1b22b40d45..6075a5d878d 100644
--- a/tools/emboss_5/emboss_geecee.xml
+++ b/tools/emboss_5/emboss_geecee.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: geecee41" name="geecee" version="5.0.0">
   <description>Calculates fractional GC content of nucleic acid sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>geecee -sequence $input1 -outfile $out_file1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_getorf.xml b/tools/emboss_5/emboss_getorf.xml
index 03f2099db7b..82da6d87b89 100644
--- a/tools/emboss_5/emboss_getorf.xml
+++ b/tools/emboss_5/emboss_getorf.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: getorf42" name="getorf" version="5.0.0">
   <description>Finds and extracts open reading frames (ORFs)</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>getorf -sequence $input1 -outseq $out_file1 -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking
   -osformat2 $out_format1 -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_helixturnhelix.xml b/tools/emboss_5/emboss_helixturnhelix.xml
index 43f875496be..6b9bbbaa67b 100644
--- a/tools/emboss_5/emboss_helixturnhelix.xml
+++ b/tools/emboss_5/emboss_helixturnhelix.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: helixturnhelix43" name="helixturnhelix" version="5.0.0">
   <description>Report nucleic acid binding motifs</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>helixturnhelix -sequence $input1 -outfile $out_file1 -mean $mean -sd $sd -minsd $minsd -eightyseven $eightyseven -rformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_hmoment.xml b/tools/emboss_5/emboss_hmoment.xml
index 24e8c2c64e8..ad4903d7bd8 100644
--- a/tools/emboss_5/emboss_hmoment.xml
+++ b/tools/emboss_5/emboss_hmoment.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: hmoment44" name="hmoment" version="5.0.0">
   <description>Hydrophobic moment calculation</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>hmoment -seqall $input1 -outfile $out_file1 -window $window -aangle $aangle -graph png -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_iep.xml b/tools/emboss_5/emboss_iep.xml
index 843c61a6972..c138ab61a3d 100644
--- a/tools/emboss_5/emboss_iep.xml
+++ b/tools/emboss_5/emboss_iep.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: iep45" name="iep" version="5.0.0">
   <description>Calculates the isoelectric point of a protein</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>iep -sequence $input1 -outfile $out_file1 -step $step -amino $amino -graph png -termini $termini -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_infoseq.xml b/tools/emboss_5/emboss_infoseq.xml
index ca172b23615..3514d8d8b1e 100644
--- a/tools/emboss_5/emboss_infoseq.xml
+++ b/tools/emboss_5/emboss_infoseq.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: infoseq46" name="infoseq" version="5.0.0">
   <!-- info contains file information always -->
   <description>Displays some simple information about sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>infoseq -sequence $input1 -outfile $out_file1 -html $html_out1 -heading $heading -usa $usa -name $disname -accession $accession -gi $gi -version $version -type $type -length $length -pgc
   $pgc -description $description -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_isochore.xml b/tools/emboss_5/emboss_isochore.xml
index b505deb97fc..acf51a9d779 100644
--- a/tools/emboss_5/emboss_isochore.xml
+++ b/tools/emboss_5/emboss_isochore.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: isochore47" name="isochore" version="5.0.0">
   <description>Plots isochores in large DNA sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -outfile $ofile2 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>
   <!--  <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>-->
   <inputs>
diff --git a/tools/emboss_5/emboss_lindna.xml b/tools/emboss_5/emboss_lindna.xml
index 78b83ce5c30..9c8a1e4d71f 100644
--- a/tools/emboss_5/emboss_lindna.xml
+++ b/tools/emboss_5/emboss_lindna.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: lindna48" name="lindna" version="5.0.0">
   <!-- tool produces memory error in ajmem.c -->
   <description>Draws linear maps of DNA constructs</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>lindna -infile $input1 -graphout png -goutfile $out_file1 -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour
   -interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight
   $rangeheight -gapgroup $gapgroup -postext $postext -auto</command>
diff --git a/tools/emboss_5/emboss_marscan.xml b/tools/emboss_5/emboss_marscan.xml
index 85979f5d26c..38c1b93e142 100644
--- a/tools/emboss_5/emboss_marscan.xml
+++ b/tools/emboss_5/emboss_marscan.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: marscan49" name="marscan" version="5.0.0">
   <description>Finds MAR/SAR sites in nucleic sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>marscan -sequence $input1 -outfile $out_file1 -rformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_maskfeat.xml b/tools/emboss_5/emboss_maskfeat.xml
index d617bbaf133..83bd477ecc7 100644
--- a/tools/emboss_5/emboss_maskfeat.xml
+++ b/tools/emboss_5/emboss_maskfeat.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: maskfeat50" name="maskfeat" version="5.0.0">
   <description>Mask off features of a sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>maskfeat -sequence $input1 -outseq $out_file1 -type "$type" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_maskseq.xml b/tools/emboss_5/emboss_maskseq.xml
index 3dfd0ddb55f..c04ff8177ce 100644
--- a/tools/emboss_5/emboss_maskseq.xml
+++ b/tools/emboss_5/emboss_maskseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: maskseq51" name="maskseq" version="5.0.0">
   <description>Mask off regions of a sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>maskseq -sequence $input1 -outseq $out_file1 -regions "$regions" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_matcher.xml b/tools/emboss_5/emboss_matcher.xml
index 744c44e4207..a5c078e7b0b 100644
--- a/tools/emboss_5/emboss_matcher.xml
+++ b/tools/emboss_5/emboss_matcher.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: matcher52" name="matcher" version="5.0.0">
   <description>Finds the best local alignments between two sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_megamerger.xml b/tools/emboss_5/emboss_megamerger.xml
index 9395d3a44de..6b8d7da646d 100644
--- a/tools/emboss_5/emboss_megamerger.xml
+++ b/tools/emboss_5/emboss_megamerger.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: megamerger53" name="megamerger" version="5.0.0">
   <description>Merge two large overlapping nucleic acid sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>megamerger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -wordsize $wordsize -prefer $prefer -osformat3 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_merger.xml b/tools/emboss_5/emboss_merger.xml
index 246e6c56383..4e21cb54a0e 100644
--- a/tools/emboss_5/emboss_merger.xml
+++ b/tools/emboss_5/emboss_merger.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: merger54" name="merger" version="5.0.0">
   <description>Merge two overlapping nucleic acid sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>merger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_msbar.xml b/tools/emboss_5/emboss_msbar.xml
index 4b9f96694c5..d60007d7afb 100644
--- a/tools/emboss_5/emboss_msbar.xml
+++ b/tools/emboss_5/emboss_msbar.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: msbar55" name="msbar" version="5.0.0">
   <description>Mutate sequence beyond all recognition</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>msbar -sequence $input1 -outseq $out_file1 -count $count -point $point -block $block -codon $codon -inframe $inframe -minimum $minimum -maximum $maximum -osformat2 $out_format1
   -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_needle.xml b/tools/emboss_5/emboss_needle.xml
index b787dd0a669..a6b1df195d6 100644
--- a/tools/emboss_5/emboss_needle.xml
+++ b/tools/emboss_5/emboss_needle.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: needle56" name="needle" version="5.0.0">
   <description>Needleman-Wunsch global alignment</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>needle -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen $gapopen -gapextend $gapextend -brief $brief -aformat3 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_newcpgreport.xml b/tools/emboss_5/emboss_newcpgreport.xml
index 271b70293b5..347dbb42b71 100644
--- a/tools/emboss_5/emboss_newcpgreport.xml
+++ b/tools/emboss_5/emboss_newcpgreport.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0">
   <description>Report CpG rich areas</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_newcpgseek.xml b/tools/emboss_5/emboss_newcpgseek.xml
index 6d1e9a935d1..dbb4897acc7 100644
--- a/tools/emboss_5/emboss_newcpgseek.xml
+++ b/tools/emboss_5/emboss_newcpgseek.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: newcpgseek58" name="newcpgseek" version="5.0.0">
   <description>Reports CpG rich region</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>newcpgseek -sequence $input1 -outfile $out_file1 -score $score -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_newseq.xml b/tools/emboss_5/emboss_newseq.xml
index 2b99403e712..9398a727ff7 100644
--- a/tools/emboss_5/emboss_newseq.xml
+++ b/tools/emboss_5/emboss_newseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: newseq59" name="newseq" version="5.0.0">
   <description>Type in a short new sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>newseq -outseq $out_file1 -name "$seqname" -description "$description" -type $type -sequence "$sequence" -osformat5 $out_format1 -auto</command>
   <inputs>
     <param name="seqname" size="10" type="text" value="">
diff --git a/tools/emboss_5/emboss_noreturn.xml b/tools/emboss_5/emboss_noreturn.xml
index 2ecd42cb8dd..b2c53a509ba 100644
--- a/tools/emboss_5/emboss_noreturn.xml
+++ b/tools/emboss_5/emboss_noreturn.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: noreturn60" name="noreturn" version="5.0.0">
   <description>Removes carriage return from ASCII files</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>noreturn -infile $input1 -outfile $out_file1 -system $system -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_notseq.xml b/tools/emboss_5/emboss_notseq.xml
index 725f2014f93..af6b71d2b26 100644
--- a/tools/emboss_5/emboss_notseq.xml
+++ b/tools/emboss_5/emboss_notseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: notseq61" name="notseq" version="5.0.0">
   <description>Exclude a set of sequences and write out the remaining ones</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>notseq -sequence $input1 -outseq $out_file1 -exclude "$exclude" -osformat3 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_nthseq.xml b/tools/emboss_5/emboss_nthseq.xml
index 1fdfc90c315..4ad61001336 100644
--- a/tools/emboss_5/emboss_nthseq.xml
+++ b/tools/emboss_5/emboss_nthseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: nthseq62" name="nthseq" version="5.0.0">
   <description>Writes one sequence from a multiple set of sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>nthseq -sequence $input1 -outseq $out_file1 -number $number -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_octanol.xml b/tools/emboss_5/emboss_octanol.xml
index 6efd6bbbbf1..0099648ff8c 100644
--- a/tools/emboss_5/emboss_octanol.xml
+++ b/tools/emboss_5/emboss_octanol.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: octanol63" name="octanol" version="5.0.0">
   <!-- graphics output with filename, no functional tests added -->  
   <description>Displays protein hydropathy</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl octanol -sequence $input1 -graph png -goutfile $out_file1 -width $width -octanolplot $octanolplot -interfaceplot $interfaceplot
   -differenceplot $differenceplot -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_oddcomp.xml b/tools/emboss_5/emboss_oddcomp.xml
index 44e2e941b01..fe5b9b31916 100644
--- a/tools/emboss_5/emboss_oddcomp.xml
+++ b/tools/emboss_5/emboss_oddcomp.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0">
   <!-- output contains file location info, commented out functional tests -->
   <description>Find protein sequence regions with a biased composition</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_palindrome.xml b/tools/emboss_5/emboss_palindrome.xml
index e9c2706015f..fc17ad508f6 100644
--- a/tools/emboss_5/emboss_palindrome.xml
+++ b/tools/emboss_5/emboss_palindrome.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0">
   <description>Looks for inverted repeats in a nucleotide sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_pasteseq.xml b/tools/emboss_5/emboss_pasteseq.xml
index b040f7fb72c..529b37c6ba5 100644
--- a/tools/emboss_5/emboss_pasteseq.xml
+++ b/tools/emboss_5/emboss_pasteseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: pasteseq66" name="pasteseq" version="5.0.0">
   <description>Insert one sequence into another</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>pasteseq -asequence $input2 -bsequence $input1 -outseq $out_file1 -pos $pos -osformat3 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_patmatdb.xml b/tools/emboss_5/emboss_patmatdb.xml
index 9930d7cc8e8..57ccce74217 100644
--- a/tools/emboss_5/emboss_patmatdb.xml
+++ b/tools/emboss_5/emboss_patmatdb.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: patmatdb67" name="patmatdb" version="5.0.0">
   <description>Search a protein sequence with a motif</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>patmatdb -sequence $input1 -outfile $out_file1 -motif "$motif" -rformat3 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_pepcoil.xml b/tools/emboss_5/emboss_pepcoil.xml
index 6bcb1a2431d..0e567d5285b 100644
--- a/tools/emboss_5/emboss_pepcoil.xml
+++ b/tools/emboss_5/emboss_pepcoil.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: pepcoil68" name="pepcoil" version="5.0.0">
   <description>Predicts coiled coil regions</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>pepcoil -sequence $input1 -outfile $out_file1 -window $window -coil $coil -frame $frame -other $other -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_pepinfo.xml b/tools/emboss_5/emboss_pepinfo.xml
index aeef0d76b92..9cd98bafd07 100644
--- a/tools/emboss_5/emboss_pepinfo.xml
+++ b/tools/emboss_5/emboss_pepinfo.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: pepinfo69" name="pepinfo" version="5.0.0">
   <!-- puts file info in output files -->
   <description>Plots simple amino acid properties in parallel</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepinfo -sequence $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -hwindow $hwindow $plot_type -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_pepnet.xml b/tools/emboss_5/emboss_pepnet.xml
index 4367467f4ae..32ab1625adb 100644
--- a/tools/emboss_5/emboss_pepnet.xml
+++ b/tools/emboss_5/emboss_pepnet.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: pepnet70" name="pepnet" version="5.0.0">
   <!-- graphical output file with path information -->
   <description>Displays proteins as a helical net</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>pepnet -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic $amphipathic -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_pepstats.xml b/tools/emboss_5/emboss_pepstats.xml
index c22399b51ef..1eae46f4cd6 100644
--- a/tools/emboss_5/emboss_pepstats.xml
+++ b/tools/emboss_5/emboss_pepstats.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: pepstats71" name="pepstats" version="5.0.0">
   <description>Protein statistics</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>pepstats -sequence $input1 -outfile $out_file1 -termini $termini -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_pepwheel.xml b/tools/emboss_5/emboss_pepwheel.xml
index 7c9a7dab993..53324fc38d4 100644
--- a/tools/emboss_5/emboss_pepwheel.xml
+++ b/tools/emboss_5/emboss_pepwheel.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0">
   <!-- produces png file -->
   <description>Shows protein sequences as helices</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic
   $amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_pepwindow.xml b/tools/emboss_5/emboss_pepwindow.xml
index afec75b3b4a..033aa262ef0 100644
--- a/tools/emboss_5/emboss_pepwindow.xml
+++ b/tools/emboss_5/emboss_pepwindow.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: pepwindow73" name="pepwindow" version="5.0.0">
   <!-- produces png file -->
   <description>Displays protein hydropathy</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwindow -sequence $input1 -graph png -goutfile $out_file1 -length $length -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_pepwindowall.xml b/tools/emboss_5/emboss_pepwindowall.xml
index b1c3d1b8ccb..cd9d3548b59 100644
--- a/tools/emboss_5/emboss_pepwindowall.xml
+++ b/tools/emboss_5/emboss_pepwindowall.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: pepwindowall74" name="pepwindowall" version="5.0.0">
   <!-- produces png file -->
   <description>Displays protein hydropathy of a set of sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwindowall -sequence $input1 -graph png -goutfile $out_file1 -length $length -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_plotcon.xml b/tools/emboss_5/emboss_plotcon.xml
index ec2be7575de..186d8453b6b 100644
--- a/tools/emboss_5/emboss_plotcon.xml
+++ b/tools/emboss_5/emboss_plotcon.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: plotcon75" name="plotcon" version="5.0.0">
   <!-- produces png file -->
   <description>Plot quality of conservation of a sequence alignment</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotcon -sequences $input1 -graph png -goutfile $out_file1 -winsize $winsize -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_plotorf.xml b/tools/emboss_5/emboss_plotorf.xml
index 0628ba9b27f..c2010dd1707 100644
--- a/tools/emboss_5/emboss_plotorf.xml
+++ b/tools/emboss_5/emboss_plotorf.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: plotorf76" name="plotorf" version="5.0.0">
   <!-- produces png file output -->
   <description>Plot potential open reading frames</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotorf -sequence $input1 -graph png -goutfile $out_file1 -start $start -stop $stop -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_polydot.xml b/tools/emboss_5/emboss_polydot.xml
index c30b79b1ad1..309e72efa5e 100644
--- a/tools/emboss_5/emboss_polydot.xml
+++ b/tools/emboss_5/emboss_polydot.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: polydot77" name="polydot" version="5.0.0">
   <!-- produces png file, not added functional tests -->
   <description>Displays all-against-all dotplots of a set of sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl polydot -sequence $input1 -graph png -goutfile $output2 -outfeat $output1 -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap
   $gap -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_preg.xml b/tools/emboss_5/emboss_preg.xml
index 86d374cc21c..ddc328522d9 100644
--- a/tools/emboss_5/emboss_preg.xml
+++ b/tools/emboss_5/emboss_preg.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: preg78" name="preg" version="5.0.0">
   <description>Regular expression search of a protein sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>preg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_prettyplot.xml b/tools/emboss_5/emboss_prettyplot.xml
index 00ac91bdd09..c6a03efc7b5 100644
--- a/tools/emboss_5/emboss_prettyplot.xml
+++ b/tools/emboss_5/emboss_prettyplot.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0">
   <!-- produces png output with file name -->
   <description>Displays aligned sequences, with colouring and boxing</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>prettyplot -sequences $input1 -graph png -goutfile $out_file1 -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity $cidentity -csimilarity $csimilarity
   -cother $cother -docolour $docolour -gtitle $title -pair $pair -identity $identity -box $box -boxcol $boxcol -boxcolval $boxcolval -name $name -maxnamelen $maxnamelen -number $number -listoptions
   $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command>
diff --git a/tools/emboss_5/emboss_prettyseq.xml b/tools/emboss_5/emboss_prettyseq.xml
index be0799bb62d..00527bc85ac 100644
--- a/tools/emboss_5/emboss_prettyseq.xml
+++ b/tools/emboss_5/emboss_prettyseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: prettyseq80" name="prettyseq" version="5.0.0">
   <description>Output sequence with translated ranges</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>prettyseq -sequence $input1 -outfile $out_file1 -ruler $ruler -plabel $plabel -nlabel $nlabel -width $width -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_primersearch.xml b/tools/emboss_5/emboss_primersearch.xml
index 6ba4cbcadb8..d7427b294f7 100644
--- a/tools/emboss_5/emboss_primersearch.xml
+++ b/tools/emboss_5/emboss_primersearch.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: primersearch81" name="primersearch" version="5.0.0">
   <description>Searches DNA sequences for matches with primer pairs</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>primersearch -seqall $input1 -infile $input2 -outfile $out_file1 -mismatchpercent $mismatchpercent -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_revseq.xml b/tools/emboss_5/emboss_revseq.xml
index 2970cb3ed61..ae7874ab988 100644
--- a/tools/emboss_5/emboss_revseq.xml
+++ b/tools/emboss_5/emboss_revseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: revseq82" name="revseq" version="5.0.0">
   <description>Reverse and complement a sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>revseq -sequence $input1 -outseq $out_file1 -reverse $reverse -complement $complement -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_seqmatchall.xml b/tools/emboss_5/emboss_seqmatchall.xml
index ee425d4e696..f50bba93bfe 100644
--- a/tools/emboss_5/emboss_seqmatchall.xml
+++ b/tools/emboss_5/emboss_seqmatchall.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: seqmatchall83" name="seqmatchall" version="5.0.0">
   <description>All-against-all comparison of a set of sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>seqmatchall -sequence $input1 -outfile $out_file1 -wordsize $wordsize -aformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_seqret.xml b/tools/emboss_5/emboss_seqret.xml
index f9f7f96cf8f..da43ba9487b 100644
--- a/tools/emboss_5/emboss_seqret.xml
+++ b/tools/emboss_5/emboss_seqret.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: seqret84" name="seqret" version="5.0.0">
   <description>Reads and writes sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>seqret -sequence $input1 -outseq $out_file1 -feature $feature -firstonly $firstonly -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_showfeat.xml b/tools/emboss_5/emboss_showfeat.xml
index b99cdf74f06..6c45dfa2be0 100644
--- a/tools/emboss_5/emboss_showfeat.xml
+++ b/tools/emboss_5/emboss_showfeat.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0">
   <!-- tool gives memory errors -->
   <description>Show features of a sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>showfeat -sequence $input1 -outfile $out_file1 -matchsource "$matchsource" -matchtype "$matchtype" -matchtag "$matchtag" -matchvalue "$matchvalue" -sort $sort -annotation "$annotation" -id
   $id -description "$description" -scale "$scale" -width "$width" -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type
   $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto</command>
diff --git a/tools/emboss_5/emboss_shuffleseq.xml b/tools/emboss_5/emboss_shuffleseq.xml
index 2c85b4f7a18..4fbaffedc4e 100644
--- a/tools/emboss_5/emboss_shuffleseq.xml
+++ b/tools/emboss_5/emboss_shuffleseq.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: shuffleseq87" name="shuffleseq" version="5.0.0">
   <!-- produces random outputs each time -->
   <description>Shuffles a set of sequences maintaining composition</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>shuffleseq -sequence $input1 -outseq $out_file1 -shuffle "$shuffle" -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_sigcleave.xml b/tools/emboss_5/emboss_sigcleave.xml
index 5c5953be302..4185200b921 100644
--- a/tools/emboss_5/emboss_sigcleave.xml
+++ b/tools/emboss_5/emboss_sigcleave.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: sigcleave88" name="sigcleave" version="5.0.0">
   <description>Reports protein signal cleavage sites</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>sigcleave -sequence $input1 -outfile $out_file1 -minweight "$minweight" -prokaryote $prokaryote -rformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_sirna.xml b/tools/emboss_5/emboss_sirna.xml
index 1370f8111f7..ca41b83ca6d 100644
--- a/tools/emboss_5/emboss_sirna.xml
+++ b/tools/emboss_5/emboss_sirna.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: sirna89" name="sirna" version="5.0.0">
   <description>Finds siRNA duplexes in mRNA</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>sirna -sequence $input1 -outfile $ofile1 -outseq $ofile2 -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2
   -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_sixpack.xml b/tools/emboss_5/emboss_sixpack.xml
index c5b22c49dbf..12baec5a5e5 100644
--- a/tools/emboss_5/emboss_sixpack.xml
+++ b/tools/emboss_5/emboss_sixpack.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0">
   <!-- tool adds file description and timestamp to output data -->
   <description>Display a DNA sequence with 6-frame translation and ORFs</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <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>
   <inputs>
diff --git a/tools/emboss_5/emboss_skipseq.xml b/tools/emboss_5/emboss_skipseq.xml
index f9ab5c5da0f..b44636e9b6c 100644
--- a/tools/emboss_5/emboss_skipseq.xml
+++ b/tools/emboss_5/emboss_skipseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: skipseq91" name="skipseq" version="5.0.0">
   <description>Reads and writes sequences, skipping first few</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>skipseq -sequence $input1 -outseq $out_file1 -skip "$skip" -feature $feature -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_splitter.xml b/tools/emboss_5/emboss_splitter.xml
index b375a1ef2db..111e77d4516 100644
--- a/tools/emboss_5/emboss_splitter.xml
+++ b/tools/emboss_5/emboss_splitter.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: splitter92" name="splitter" version="5.0.0">
   <description>Split a sequence into (overlapping) smaller sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>splitter -sequence $input1 -outseq $out_file1 -size "$size" -overlap "$overlap" -addoverlap $addoverlap -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_supermatcher.xml b/tools/emboss_5/emboss_supermatcher.xml
index 3bb225b4e43..6022cd316fa 100644
--- a/tools/emboss_5/emboss_supermatcher.xml
+++ b/tools/emboss_5/emboss_supermatcher.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: supermatcher95" name="supermatcher" version="5.0.0">
   <!-- puts file information in output report -->
   <description>Match large sequences against one or more other sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>supermatcher -asequence $input1 -bsequence $input2 -gapopen "$gapopen" -gapextend "$gapextend" -width "$width" -wordlen "$wordlen" -outfile $ofile1 -errorfile $ofile2 -aformat3
   $out_format1 -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_syco.xml b/tools/emboss_5/emboss_syco.xml
index 001603e3e97..43670e2ba59 100644
--- a/tools/emboss_5/emboss_syco.xml
+++ b/tools/emboss_5/emboss_syco.xml
@@ -1,6 +1,7 @@
 <tool id="EMBOSS: syco96" name="syco" version="5.0.0">
   <!-- graphics output -->
   <description>Synonymous codon usage Gribskov statistic plot</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl syco -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -cfile $cfile -window "$window" -uncommon $uncommon -minimum "$minimum"
   -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_tcode.xml b/tools/emboss_5/emboss_tcode.xml
index 0f609e9079d..2e4eb8311e3 100644
--- a/tools/emboss_5/emboss_tcode.xml
+++ b/tools/emboss_5/emboss_tcode.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: tcode97" name="tcode" version="5.0.0">
   <description>Fickett TESTCODE statistic to identify protein-coding DNA</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>tcode -sequence $input1 -outfile $out_file1 -window "$window" -step "$step" -rformat $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_textsearch.xml b/tools/emboss_5/emboss_textsearch.xml
index 1925d619027..15523f190eb 100644
--- a/tools/emboss_5/emboss_textsearch.xml
+++ b/tools/emboss_5/emboss_textsearch.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: textsearch98" name="textsearch" version="5.0.0">
   <description>Search sequence documentation. Slow, use SRS and Entrez!</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>textsearch -sequence $input1 -outfile $out_file1 -pattern "$pattern" -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html
   $html_out1 -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_tmap.xml b/tools/emboss_5/emboss_tmap.xml
index df6d3208ff0..1f34f374afc 100644
--- a/tools/emboss_5/emboss_tmap.xml
+++ b/tools/emboss_5/emboss_tmap.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: tmap99" name="tmap" version="5.0.0">
   <description>Displays membrane spanning regions</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl tmap -sequences $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -rformat $out_format1 -auto</command>
   <inputs>
     <param format="data" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_tranalign.xml b/tools/emboss_5/emboss_tranalign.xml
index a6d422260d9..2d820c55f10 100644
--- a/tools/emboss_5/emboss_tranalign.xml
+++ b/tools/emboss_5/emboss_tranalign.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0">
   <description>Align nucleic coding regions given the aligned proteins</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>tranalign -asequence $input1 -bsequence $input2 -outseq $out_file1 -table $table -osformat3 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_transeq.xml b/tools/emboss_5/emboss_transeq.xml
index f5cf28d1913..978b56571cb 100644
--- a/tools/emboss_5/emboss_transeq.xml
+++ b/tools/emboss_5/emboss_transeq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: transeq101" name="transeq" version="5.0.0">
   <description>Translate nucleic acid sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>transeq -sequence $input1 -outseq $out_file1 -frame $frame -table $table -regions "$regions" -trim $trim -clean $clean -alternative $alternative -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_trimest.xml b/tools/emboss_5/emboss_trimest.xml
index 07a096981ec..0f128b76202 100644
--- a/tools/emboss_5/emboss_trimest.xml
+++ b/tools/emboss_5/emboss_trimest.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: trimest102" name="trimest" version="5.0.0">
   <description>Trim poly-A tails off EST sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>trimest -sequence $input1 -outseq $out_file1 -minlength "$minlength" -mismatches "$mismatches" -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1
   -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_trimseq.xml b/tools/emboss_5/emboss_trimseq.xml
index dea6018b1ed..23fb327d0c4 100644
--- a/tools/emboss_5/emboss_trimseq.xml
+++ b/tools/emboss_5/emboss_trimseq.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: trimseq103" name="trimseq" version="5.0.0">
   <description>Trim ambiguous bits off the ends of sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>trimseq -sequence $input1 -outseq $out_file1 -window "$window" -percent "$percent" -strict $strict -star $star -left $left -right $right -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_twofeat.xml b/tools/emboss_5/emboss_twofeat.xml
index b21cabf6c19..7d2bed77496 100644
--- a/tools/emboss_5/emboss_twofeat.xml
+++ b/tools/emboss_5/emboss_twofeat.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0">
   <description>Finds neighbouring pairs of features in sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>twofeat -sequence $input1 -outfile $out_file1 -atype "$atype" -btype "$btype" -minrange "$minrange" -maxrange "$maxrange" -asource "$asource" -asense $asense -aminscore "$aminscore"
   -amaxscore "$amaxscore" -atag "$atag" -avalue "$avalue" -bsource "$bsource" -bsense "$bsense" -bminscore "$bminscore" -bmaxscore "$bmaxscore" -btag "$btag" -bvalue "$bvalue" -overlap $overlap
   -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout "$typeout" -rformat2 $out_format1 -auto</command>
diff --git a/tools/emboss_5/emboss_union.xml b/tools/emboss_5/emboss_union.xml
index 20f7be665d7..5ea8e4dc116 100644
--- a/tools/emboss_5/emboss_union.xml
+++ b/tools/emboss_5/emboss_union.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: union105" name="union" version="5.0.0">
   <description>Reads sequence fragments and builds one sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>union -sequence $input1 -outseq $out_file1 -osformat2 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_vectorstrip.xml b/tools/emboss_5/emboss_vectorstrip.xml
index ca30d125e0f..960645147ee 100644
--- a/tools/emboss_5/emboss_vectorstrip.xml
+++ b/tools/emboss_5/emboss_vectorstrip.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="5.0.0">
   <description>Strips out DNA between a pair of vector sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>vectorstrip -sequence $input1 -vectorsfile $input2 -outseq $ofile1 -outfile $ofile2 -vectorfile yes -mismatch "$mismatch" -besthits $besthits -linkera "$linkera" -linkerb
   "$linkerb" -osformat4 $out_format1 -auto</command>
   <inputs>
diff --git a/tools/emboss_5/emboss_water.xml b/tools/emboss_5/emboss_water.xml
index 565509682fc..bf589cf319d 100644
--- a/tools/emboss_5/emboss_water.xml
+++ b/tools/emboss_5/emboss_water.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: water107" name="water" version="5.0.0">
   <description>Smith-Waterman local alignment</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>water -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen "$gapopen" -gapextend "$gapextend" -brief $brief -aformat3 $out_format1 -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_wobble.xml b/tools/emboss_5/emboss_wobble.xml
index 93370911c8a..a4dd0cf76c2 100644
--- a/tools/emboss_5/emboss_wobble.xml
+++ b/tools/emboss_5/emboss_wobble.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: wobble108" name="wobble" version="5.0.0">
   <description>Wobble base plot</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command interpreter="perl">emboss_single_outputfile_wrapper.pl wobble -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -window "$window" -bases "$bases" -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_wordcount.xml b/tools/emboss_5/emboss_wordcount.xml
index 5f1b63508d5..db4e15f3942 100644
--- a/tools/emboss_5/emboss_wordcount.xml
+++ b/tools/emboss_5/emboss_wordcount.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: wordcount109" name="wordcount" version="5.0.0">
   <description>Counts words of a specified size in a DNA sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>wordcount -sequence $input1 -outfile $out_file1 -wordsize "$wordsize" -auto</command>
   <inputs>
     <param format="fasta" name="input1" type="data">
diff --git a/tools/emboss_5/emboss_wordmatch.xml b/tools/emboss_5/emboss_wordmatch.xml
index 9d539665e97..d4c70ffd2e7 100644
--- a/tools/emboss_5/emboss_wordmatch.xml
+++ b/tools/emboss_5/emboss_wordmatch.xml
@@ -1,5 +1,6 @@
 <tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0">
   <description>Finds all exact matches of a given size between 2 sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2
   -offormat5 $out_format3 -auto</command>
   <inputs>
diff --git a/tools/evolution/add_scores.xml b/tools/evolution/add_scores.xml
index de272cf3607..51cd75b82fc 100644
--- a/tools/evolution/add_scores.xml
+++ b/tools/evolution/add_scores.xml
@@ -17,7 +17,7 @@
   </outputs>
 
   <requirements>
-    <requirement type="binary">add_scores</requirement>
+    <requirement type="package">add_scores</requirement>
   </requirements>
 
   <tests>
diff --git a/tools/evolution/codingSnps.xml b/tools/evolution/codingSnps.xml
index 3fde8063af5..c9c8ccdf4ac 100644
--- a/tools/evolution/codingSnps.xml
+++ b/tools/evolution/codingSnps.xml
@@ -24,7 +24,7 @@
   <requirements>
     <requirement type="binary">cat</requirement>
     <requirement type="binary">sort</requirement>
-    <requirement type="binary">twoBitToFa</requirement>
+    <requirement type="package">ucsc_tools</requirement>
   </requirements>
 
   <tests>
diff --git a/tools/extract/liftOver_wrapper.xml b/tools/extract/liftOver_wrapper.xml
index 482df43e6ba..2615f6aa615 100644
--- a/tools/extract/liftOver_wrapper.xml
+++ b/tools/extract/liftOver_wrapper.xml
@@ -30,7 +30,7 @@
     <data format="input" name="out_file2" label="${tool.name} on ${on_string} [ UNMAPPED COORDINATES ]" />
   </outputs>
   <requirements>
-    <requirement type="binary">liftOver</requirement>
+    <requirement type="package">ucsc_tools</requirement>
   </requirements>
   <tests>
     <test>
diff --git a/tools/fastx_toolkit/fasta_clipping_histogram.xml b/tools/fastx_toolkit/fasta_clipping_histogram.xml
index 889f8046724..ac8d9107d3d 100644
--- a/tools/fastx_toolkit/fasta_clipping_histogram.xml
+++ b/tools/fastx_toolkit/fasta_clipping_histogram.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fasta_clipping_histogram" name="Length Distribution">
 	<description>chart</description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	<command>fasta_clipping_histogram.pl $input $outfile</command>
 	
 	<inputs>
diff --git a/tools/fastx_toolkit/fasta_formatter.xml b/tools/fastx_toolkit/fasta_formatter.xml
index ca916682635..799b05aead9 100644
--- a/tools/fastx_toolkit/fasta_formatter.xml
+++ b/tools/fastx_toolkit/fasta_formatter.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fasta_formatter" name="FASTA Width">
 	<description>formatter</description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	<!--
 		Note:
 			fasta_formatter also has a tabular output mode (-t),
diff --git a/tools/fastx_toolkit/fasta_nucleotide_changer.xml b/tools/fastx_toolkit/fasta_nucleotide_changer.xml
index 5f4ba1ffaee..236c0ae6d31 100644
--- a/tools/fastx_toolkit/fasta_nucleotide_changer.xml
+++ b/tools/fastx_toolkit/fasta_nucleotide_changer.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fasta_nucleotides_changer" name="RNA/DNA" >
 	<description>converter</description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	<command>zcat -f '$input' | fasta_nucleotide_changer $mode -v -o $output</command>
 	<inputs>
 		<param format="fasta" name="input" type="data" label="Library to convert" />
diff --git a/tools/fastx_toolkit/fastq_quality_boxplot.xml b/tools/fastx_toolkit/fastq_quality_boxplot.xml
index f2ce7941391..fa8363c5b3b 100644
--- a/tools/fastx_toolkit/fastq_quality_boxplot.xml
+++ b/tools/fastx_toolkit/fastq_quality_boxplot.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot">
 	<description></description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	
 	<command>fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output</command>
 	
diff --git a/tools/fastx_toolkit/fastq_quality_converter.xml b/tools/fastx_toolkit/fastq_quality_converter.xml
index 88cdf41e19b..7e0b264d8e9 100644
--- a/tools/fastx_toolkit/fastq_quality_converter.xml
+++ b/tools/fastx_toolkit/fastq_quality_converter.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fastq_quality_converter" name="Quality format converter">
 	<description>(ASCII-Numeric)</description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	<command>zcat -f $input | fastq_quality_converter $QUAL_FORMAT -o $output -Q $offset</command>
 	<inputs>
 		<param format="fastq" name="input" type="data" label="Library to convert" />
diff --git a/tools/fastx_toolkit/fastq_quality_filter.xml b/tools/fastx_toolkit/fastq_quality_filter.xml
index 94b30372b76..af8766a5506 100644
--- a/tools/fastx_toolkit/fastq_quality_filter.xml
+++ b/tools/fastx_toolkit/fastq_quality_filter.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fastq_quality_filter" name="Filter by quality">
 	<description></description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 
 	<command>zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output</command>
 
diff --git a/tools/fastx_toolkit/fastq_to_fasta.xml b/tools/fastx_toolkit/fastq_to_fasta.xml
index ccfb30453d0..3b0dcb9283a 100644
--- a/tools/fastx_toolkit/fastq_to_fasta.xml
+++ b/tools/fastx_toolkit/fastq_to_fasta.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA">
 	<description>converter</description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	<command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v </command>
 
 	<inputs>
diff --git a/tools/fastx_toolkit/fastx_artifacts_filter.xml b/tools/fastx_toolkit/fastx_artifacts_filter.xml
index 48e06cffb1f..4980f7622f4 100644
--- a/tools/fastx_toolkit/fastx_artifacts_filter.xml
+++ b/tools/fastx_toolkit/fastx_artifacts_filter.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fastx_artifacts_filter" name="Remove sequencing artifacts">
 	<description></description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	<command>zcat -f '$input' | fastx_artifacts_filter -v -o "$output"</command>
 
 	<inputs>
diff --git a/tools/fastx_toolkit/fastx_barcode_splitter.xml b/tools/fastx_toolkit/fastx_barcode_splitter.xml
index aec33946bef..1d901a13d8f 100644
--- a/tools/fastx_toolkit/fastx_barcode_splitter.xml
+++ b/tools/fastx_toolkit/fastx_barcode_splitter.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fastx_barcode_splitter" name="Barcode Splitter">
 	<description></description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	<command interpreter="sh">fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output </command>
 
 	<inputs>
diff --git a/tools/fastx_toolkit/fastx_clipper.xml b/tools/fastx_toolkit/fastx_clipper.xml
index 11c7001ec0e..087377ed3e5 100644
--- a/tools/fastx_toolkit/fastx_clipper.xml
+++ b/tools/fastx_toolkit/fastx_clipper.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fastx_clipper" name="Clip" version="1.0.1" >
   <description>adapter sequences</description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
   <command>
     zcat -f $input | fastx_clipper -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS
   </command>
diff --git a/tools/fastx_toolkit/fastx_collapser.xml b/tools/fastx_toolkit/fastx_collapser.xml
index e879ad265cd..cc4029ffd36 100644
--- a/tools/fastx_toolkit/fastx_collapser.xml
+++ b/tools/fastx_toolkit/fastx_collapser.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fastx_collapser" name="Collapse">
 	<description>sequences</description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	<command>zcat -f '$input' | fastx_collapser -v -o '$output' </command>
 
 	<inputs>
diff --git a/tools/fastx_toolkit/fastx_nucleotides_distribution.xml b/tools/fastx_toolkit/fastx_nucleotides_distribution.xml
index 5ac05bd5dec..29254e47ce7 100644
--- a/tools/fastx_toolkit/fastx_nucleotides_distribution.xml
+++ b/tools/fastx_toolkit/fastx_nucleotides_distribution.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fastx_nucleotides_distribution" name="Draw nucleotides distribution chart">
 	<description></description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	<command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command>
 	
 	<inputs>
diff --git a/tools/fastx_toolkit/fastx_quality_statistics.xml b/tools/fastx_toolkit/fastx_quality_statistics.xml
index ab0c1e47f84..4126a9727a9 100644
--- a/tools/fastx_toolkit/fastx_quality_statistics.xml
+++ b/tools/fastx_toolkit/fastx_quality_statistics.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fastx_quality_statistics" name="Compute quality statistics">
 	<description></description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	<command>zcat -f $input | fastx_quality_stats -o $output -Q 33</command>
 
 	<inputs>
diff --git a/tools/fastx_toolkit/fastx_renamer.xml b/tools/fastx_toolkit/fastx_renamer.xml
index 51d1366cbd9..258ec2541bb 100644
--- a/tools/fastx_toolkit/fastx_renamer.xml
+++ b/tools/fastx_toolkit/fastx_renamer.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" >
 	<description></description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	<command>zcat -f $input | fastx_renamer -n $TYPE -o $output -v </command>
 
 	<inputs>
diff --git a/tools/fastx_toolkit/fastx_reverse_complement.xml b/tools/fastx_toolkit/fastx_reverse_complement.xml
index fe4a67e1913..66bb54f38ce 100644
--- a/tools/fastx_toolkit/fastx_reverse_complement.xml
+++ b/tools/fastx_toolkit/fastx_reverse_complement.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
 	<description></description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	<command>zcat -f '$input' | fastx_reverse_complement -v -o $output</command>
 	<inputs>
 		<param format="fasta,fastqsolexa" name="input" type="data" label="Library to reverse-complement" />
diff --git a/tools/fastx_toolkit/fastx_trimmer.xml b/tools/fastx_toolkit/fastx_trimmer.xml
index 797407829fb..f559121320a 100644
--- a/tools/fastx_toolkit/fastx_trimmer.xml
+++ b/tools/fastx_toolkit/fastx_trimmer.xml
@@ -1,5 +1,6 @@
 <tool id="cshl_fastx_trimmer" name="Trim sequences">
 	<description></description>
+	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 	<command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output</command>
 
 	<inputs>
diff --git a/tools/filters/wig_to_bigwig.xml b/tools/filters/wig_to_bigwig.xml
index 50431e6e843..77e0620db75 100644
--- a/tools/filters/wig_to_bigwig.xml
+++ b/tools/filters/wig_to_bigwig.xml
@@ -2,7 +2,7 @@
   <description>converter</description>
   <command>grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 -blockSize=$blockSize -itemsPerSlot=$itemsPerSlot $clip $unc 2&gt;&amp;1 || echo "Error running wigToBigWig." >&amp;2</command>
   <requirements>
-    <requirement type="binary">wigToBigWig</requirement>
+    <requirement type="package">ucsc_tools</requirement>
   </requirements>
   <inputs>
     <param format="wig" name="input1" type="data" label="Convert">
diff --git a/tools/metag_tools/megablast_wrapper.xml b/tools/metag_tools/megablast_wrapper.xml
index 1b440da51e1..ec2a654b60c 100644
--- a/tools/metag_tools/megablast_wrapper.xml
+++ b/tools/metag_tools/megablast_wrapper.xml
@@ -34,7 +34,7 @@
         <data name="output1" format="tabular"/>
     </outputs>
     <requirements>
-        <requirement type="binary">megablast</requirement>
+        <requirement type="package">megablast</requirement>
     </requirements>
     <tests>
         <test>
diff --git a/tools/ngs_rna/cuffcompare_wrapper.xml b/tools/ngs_rna/cuffcompare_wrapper.xml
index a6bd3a71017..1ddaf1f0cd8 100644
--- a/tools/ngs_rna/cuffcompare_wrapper.xml
+++ b/tools/ngs_rna/cuffcompare_wrapper.xml
@@ -1,5 +1,8 @@
 <tool id="cuffcompare" name="Cuffcompare" version="0.8.3">
     <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description>
+    <requirements>
+        <requirement type="package">cufflinks</requirement>
+    </requirements>
     <command interpreter="python">
         cuffcompare_wrapper.py 
             --transcripts-accuracy-output=$transcripts_accuracy
diff --git a/tools/ngs_rna/cuffdiff_wrapper.xml b/tools/ngs_rna/cuffdiff_wrapper.xml
index 61c5e24e049..a4d36cad20a 100644
--- a/tools/ngs_rna/cuffdiff_wrapper.xml
+++ b/tools/ngs_rna/cuffdiff_wrapper.xml
@@ -1,5 +1,8 @@
 <tool id="cuffdiff" name="Cuffdiff" version="0.8.3">
     <description>find significant changes in transcript expression, splicing, and promoter use</description>
+    <requirements>
+        <requirement type="package">cufflinks</requirement>
+    </requirements>
     <command interpreter="python">
         cuffdiff_wrapper.py
             --FDR=$fdr
diff --git a/tools/ngs_rna/cufflinks_wrapper.xml b/tools/ngs_rna/cufflinks_wrapper.xml
index 7bb13253cc5..a686fbce045 100644
--- a/tools/ngs_rna/cufflinks_wrapper.xml
+++ b/tools/ngs_rna/cufflinks_wrapper.xml
@@ -1,5 +1,8 @@
 <tool id="cufflinks" name="Cufflinks" version="0.8.3">
     <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description>
+    <requirements>
+        <requirement type="package">cufflinks</requirement>
+    </requirements>
     <command interpreter="python">
         cufflinks_wrapper.py 
             --input=$input
diff --git a/tools/ngs_rna/tophat_wrapper.xml b/tools/ngs_rna/tophat_wrapper.xml
index 98b956fbfa8..2bfd17ba332 100644
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -1,5 +1,8 @@
 <tool id="tophat" name="Tophat" version="1.0.14">
     <description>Find splice junctions using RNA-seq data</description>
+    <requirements>
+        <requirement type="package">tophat</requirement>
+    </requirements>
     <command interpreter="python">
         tophat_wrapper.py
             ## Change this to accomodate the number of threads you have available.
diff --git a/tools/peak_calling/macs_wrapper.xml b/tools/peak_calling/macs_wrapper.xml
index d109e2d7864..cdd7fd8b30d 100644
--- a/tools/peak_calling/macs_wrapper.xml
+++ b/tools/peak_calling/macs_wrapper.xml
@@ -3,7 +3,6 @@
   <command interpreter="python">macs_wrapper.py $options_file $output_bed_file $output_extra_files $output_extra_files.files_path</command>
   <requirements>
     <requirement type="python-module">macs</requirement>
-    <requirement type="binary">macs</requirement>
     <requirement type="package">macs</requirement>
   </requirements>
   <inputs>
diff --git a/tools/regVariation/microsats_alignment_level.xml b/tools/regVariation/microsats_alignment_level.xml
index 92f913938f8..949f79ca440 100644
--- a/tools/regVariation/microsats_alignment_level.xml
+++ b/tools/regVariation/microsats_alignment_level.xml
@@ -22,7 +22,7 @@
     <data format="tabular" name="out_file1" metadata_source="input1"/>
   </outputs>
   <requirements>
-     <requirement type="binary">bx-sputnik</requirement>
+     <requirement type="package">sputnik</requirement>
   </requirements>
   <tests>
     <test>
@@ -58,4 +58,4 @@ This tool uses a modified version of SPUTNIK to fetch microsatellite repeats fro
 </help>  
 
 
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/sr_assembly/velvetg.xml b/tools/sr_assembly/velvetg.xml
index 4cb32da18d8..0b1cda82bef 100644
--- a/tools/sr_assembly/velvetg.xml
+++ b/tools/sr_assembly/velvetg.xml
@@ -184,7 +184,7 @@
                 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs"/>
 	</outputs>
 	<requirements>
-		<requirement type="binary">velvetg</requirement>
+		<requirement type="package">velvet</requirement>
 	</requirements>
 	<tests>
 	  <test>
diff --git a/tools/sr_assembly/velveth.xml b/tools/sr_assembly/velveth.xml
index 5b112f5bfa5..48c5ea280cd 100644
--- a/tools/sr_assembly/velveth.xml
+++ b/tools/sr_assembly/velveth.xml
@@ -48,7 +48,7 @@
                 <data format="velvet" name="out_file1" />
 	</outputs>
 	<requirements>
-		<requirement type="binary">velveth</requirement>
+		<requirement type="package">velvet</requirement>
 	</requirements>
 	<tests>
           <test>
diff --git a/tools/sr_mapping/PerM.xml b/tools/sr_mapping/PerM.xml
index 5f3bc908262..7e6e0da4e38 100644
--- a/tools/sr_mapping/PerM.xml
+++ b/tools/sr_mapping/PerM.xml
@@ -1,6 +1,9 @@
 <tool id="PerM" name="Map with PerM" version="1.0.0">
   <description>for SOLiD and Illumina</description>
   <!-- works with PerM version 0.2.6 -->
+  <requirements>
+      <requirement type="package">perm</requirement>
+  </requirements>
   <command>
 PerM
 #if $s.sourceOfRef.refSource == "history":
diff --git a/tools/sr_mapping/bfast_wrapper.xml b/tools/sr_mapping/bfast_wrapper.xml
index 8f4f2c17477..496ed1dca87 100644
--- a/tools/sr_mapping/bfast_wrapper.xml
+++ b/tools/sr_mapping/bfast_wrapper.xml
@@ -322,7 +322,7 @@ For **postprocess**::
 
   </help>
   <requirements>
-    <requirement type="binary">bfast</requirement>
+    <requirement type="package">bfast</requirement>
   </requirements>
   <tests>
     <test>
diff --git a/tools/sr_mapping/bowtie_color_wrapper.xml b/tools/sr_mapping/bowtie_color_wrapper.xml
index b8dd48f0856..3570203a806 100644
--- a/tools/sr_mapping/bowtie_color_wrapper.xml
+++ b/tools/sr_mapping/bowtie_color_wrapper.xml
@@ -1,4 +1,5 @@
 <tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.0.0">
+  <requirements><requirement type='package'>bowtie</requirement></requirements>
   <description></description>
   <command interpreter="python">
     bowtie_wrapper.py 
diff --git a/tools/sr_mapping/lastz_paired_reads_wrapper.xml b/tools/sr_mapping/lastz_paired_reads_wrapper.xml
index 9f04f47a116..fa28ee84a1e 100644
--- a/tools/sr_mapping/lastz_paired_reads_wrapper.xml
+++ b/tools/sr_mapping/lastz_paired_reads_wrapper.xml
@@ -52,7 +52,7 @@
         <data format="sam" name="output1" />
     </outputs>
     <requirements>
-        <requirement type="binary">lastz</requirement>
+        <requirement type="package">lastz</requirement>
     </requirements>
     <tests>
         <test>
diff --git a/tools/sr_mapping/lastz_wrapper.xml b/tools/sr_mapping/lastz_wrapper.xml
index 7b255e73197..7dd5424d6aa 100644
--- a/tools/sr_mapping/lastz_wrapper.xml
+++ b/tools/sr_mapping/lastz_wrapper.xml
@@ -122,7 +122,7 @@
         </data>
     </outputs>
     <requirements>
-        <requirement type="binary">lastz</requirement>
+        <requirement type="package">lastz</requirement>
     </requirements>
     <tests>
         <test>
diff --git a/tools/taxonomy/find_diag_hits.xml b/tools/taxonomy/find_diag_hits.xml
index e57cde42360..eaa95e53ccd 100644
--- a/tools/taxonomy/find_diag_hits.xml
+++ b/tools/taxonomy/find_diag_hits.xml
@@ -1,5 +1,8 @@
 <tool id="find_diag_hits" name="Find diagnostic hits" version="1.0.0">
     <description></description>
+    <requirements>
+        <requirement type="package">taxonomy</requirement>
+    </requirements>
     <command interpreter="python">find_diag_hits.py $input1 $id_col $rank_list $out_format $out_file1</command>
     <inputs>
         <param format="taxonomy" name="input1" type="data" label="Find diagnostic hits in"/>
diff --git a/tools/taxonomy/gi2taxonomy.xml b/tools/taxonomy/gi2taxonomy.xml
index 5aa68d755fa..fa95eec2729 100644
--- a/tools/taxonomy/gi2taxonomy.xml
+++ b/tools/taxonomy/gi2taxonomy.xml
@@ -1,5 +1,8 @@
 <tool id="Fetch Taxonomic Ranks" name="Fetch taxonomic representation" version="1.1.0">
   <description></description>
+    <requirements>
+        <requirement type="package">taxonomy</requirement>
+    </requirements>
   <command interpreter="python">gi2taxonomy.py $input $giField $idField $out_file1 ${GALAXY_DATA_INDEX_DIR}</command>
   <inputs>
     <param format="tabular" name="input" type="data" label="Show taxonomic representation for"></param>
diff --git a/tools/taxonomy/lca.xml b/tools/taxonomy/lca.xml
index a8f3ed91468..1f899fab74a 100644
--- a/tools/taxonomy/lca.xml
+++ b/tools/taxonomy/lca.xml
@@ -1,5 +1,8 @@
 <tool id="lca1" name="Find lowest diagnostic rank" version="1.0.1">
   <description></description>
+    <requirements>
+        <requirement type="package">taxonomy</requirement>
+    </requirements>
   <command interpreter="python">
     lca.py $input1 $out_file1 $rank_bound
   </command>
@@ -94,4 +97,4 @@ Note, that **read_2** is now omitted as it matches two phyla (**phylum3** and **
 
 
 </help>
-</tool>
\ No newline at end of file
+</tool>
diff --git a/tools/taxonomy/poisson2test.xml b/tools/taxonomy/poisson2test.xml
index a13f97185b4..dbd5145a546 100644
--- a/tools/taxonomy/poisson2test.xml
+++ b/tools/taxonomy/poisson2test.xml
@@ -1,5 +1,8 @@
 <tool id="poisson2test" name="Poisson two-sample test" version="1.0.0">
   <description></description>
+    <requirements>
+        <requirement type="package">taxonomy</requirement>
+    </requirements>
   <command interpreter="python">poisson2test.py $input1 $input2 $input3 $input4 $input5 $output1 2>/dev/null </command>
   <inputs>
     <param name="input1" format="tabular" type="data" label="Input File"/>
diff --git a/tools/taxonomy/t2ps_wrapper.xml b/tools/taxonomy/t2ps_wrapper.xml
index 8af421ed517..a923641b47f 100644
--- a/tools/taxonomy/t2ps_wrapper.xml
+++ b/tools/taxonomy/t2ps_wrapper.xml
@@ -1,5 +1,8 @@
 <tool id="Draw_phylogram" name="Draw phylogeny" version="1.0.0">
   <description></description>
+    <requirements>
+        <requirement type="package">taxonomy</requirement>
+    </requirements>
   <command interpreter="python">t2ps_wrapper.py $input $out_file1 $max_tree_level $font_size $max_leaves 1</command>
   <inputs>
     <param format="taxonomy" name="input" type="data" label="Draw phylogram for"></param>
diff --git a/tools/taxonomy/t2t_report.xml b/tools/taxonomy/t2t_report.xml
index bfaa35aceb6..6aca4f02ad9 100644
--- a/tools/taxonomy/t2t_report.xml
+++ b/tools/taxonomy/t2t_report.xml
@@ -1,5 +1,8 @@
 <tool id="t2t_report" name="Summarize taxonomy" version="1.0.0">
     <description></description>
+    <requirements>
+        <requirement type="package">taxonomy</requirement>
+    </requirements>
     <command>taxonomy2tree $input 0 /dev/null $out_file1 0 &amp;&gt; /dev/null</command>
     <inputs>
         <param format="taxonomy" name="input" type="data" label="Summarize taxonomic representation for"/>