# HG changeset patch
# User devteam
# Date 1447261961 18000
# Node ID b810c96613eeee1718609cc1ca07e2f047ce8c83
# Parent  ce22ceec214a21935168bc8f67f3083793bfb8d1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7

diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_antigenic.xml
--- a/emboss_5/emboss_antigenic.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_antigenic.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="data" name="input1" type="data">
       <label>On query</label>
     </param>
-    <param name="minlen" size="4" type="text" value="6">
+    <param name="minlen" type="text" value="6">
       <label>Minimum Length of region</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_biosed.xml
--- a/emboss_5/emboss_biosed.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_biosed.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,10 +6,10 @@
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
     </param>
-    <param name="target" size="6" type="text" value="atg">
+    <param name="target" type="text" value="atg">
       <label>Replace all</label>
     </param>
-    <param name="replace" size="6" type="text" value="atg">
+    <param name="replace" type="text" value="atg">
       <label>with</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_charge.xml
--- a/emboss_5/emboss_charge.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_charge.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
     </param>
-    <param name="window" size="4" type="text" value="5">
+    <param name="window" type="text" value="5">
       <label>Window Size</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_checktrans.xml
--- a/emboss_5/emboss_checktrans.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_checktrans.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
     </param>
-    <param name="orfml" size="4" type="text" value="100">
+    <param name="orfml" type="text" value="100">
       <label>Minimum ORF Length to report</label>
     </param>
     <param name="addlast" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_compseq.xml
--- a/emboss_5/emboss_compseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_compseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
     </param>
-    <param name="word" size="4" type="text" value="2">
+    <param name="word" type="text" value="2">
       <label>Size of word (window) to count</label>
     </param>
     <param name="frame" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_cpgplot.xml
--- a/emboss_5/emboss_cpgplot.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_cpgplot.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,16 +6,16 @@
     <param format="data" name="input1" type="data">
       <label>On query</label>
     </param>
-    <param name="window" size="4" type="integer" value="100">
+    <param name="window" type="integer" value="100">
       <label>Window Size</label>
     </param>
-    <param name="minlen" size="4" type="integer" value="200">
+    <param name="minlen" type="integer" value="200">
       <label>Minimum length</label>
     </param>
-    <param name="minoe" size="4" type="float" value="0.6">
+    <param name="minoe" type="float" value="0.6">
       <label>Minimum average observed to expected ratio</label>
     </param>
-    <param name="minpc" size="4" type="float" value="50.0">
+    <param name="minpc" type="float" value="50.0">
       <label>Minimum average percentage of G plus C</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_cpgreport.xml
--- a/emboss_5/emboss_cpgreport.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_cpgreport.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
     </param>
-    <param name="score" size="4" type="text" value="17">
+    <param name="score" type="text" value="17">
       <label>Score for each CG sequence found (1-200)</label>
     </param>
     <param name="out_format2" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_cutseq.xml
--- a/emboss_5/emboss_cutseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_cutseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,10 +6,10 @@
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
     </param>
-    <param name="from" size="8" type="text" value="1">
+    <param name="from" type="text" value="1">
       <label>Start of region to delete</label>
     </param>
-    <param name="to" size="8" type="text" value="1">
+    <param name="to" type="text" value="1">
       <label>End of region to delete</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_dan.xml
--- a/emboss_5/emboss_dan.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_dan.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -7,16 +7,16 @@
     <param format="data" name="input1" type="data">
       <label>On query</label>
     </param>
-    <param name="window" size="4" type="text" value="20">
+    <param name="window" type="text" value="20">
       <label>Window Size</label>
     </param>
-    <param name="shift" size="4" type="text" value="1">
+    <param name="shift" type="text" value="1">
       <label>Step size (shift increment)</label>
     </param>
-    <param name="dnaconc" size="4" type="text" value="50.0">
+    <param name="dnaconc" type="text" value="50.0">
       <label>DNA Concentration (nM)</label>
     </param>
-    <param name="saltconc" size="4" type="text" value="50.0">
+    <param name="saltconc" type="text" value="50.0">
       <label>Salt concentration (mM)</label>
     </param>
     <param name="thermo" type="select">
@@ -24,7 +24,7 @@
       <option value="yes">Yes</option>
       <option value="no">No</option>
     </param>
-    <param name="temperature" size="4" type="text" value="25 ">
+    <param name="temperature" type="text" value="25 ">
       <label>Temperature at which to calculate the DeltaG, DeltaH and DeltaS values</label>
     </param>
     <param name="rna" type="select">
@@ -37,13 +37,13 @@
       <option value="no">No</option>
       <option value="yes">Yes</option>
     </param>
-    <param name="formamide" size="4" type="text" value="0 ">
+    <param name="formamide" type="text" value="0 ">
       <label>Formamide concentration (nM)</label>
     </param>
-    <param name="mismatch" size="4" type="text" value="0 ">
+    <param name="mismatch" type="text" value="0 ">
       <label>Percent mismatch to be used in calculations</label>
     </param>
-    <param name="prodlen" size="4" type="text" value="20">
+    <param name="prodlen" type="text" value="20">
       <label>Product length to be used in calculations</label>
     </param>
     <param name="plot1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_descseq.xml
--- a/emboss_5/emboss_descseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_descseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,10 +6,10 @@
     <param format="data" name="input1" type="data">
       <label>On query</label>
     </param>
-    <param name="seqname" size="50" type="text" value="">
+    <param name="seqname" type="text" value="">
       <label>Name of the sequence</label>
     </param>
-    <param name="desc" size="50" type="text" value="">
+    <param name="desc" type="text" value="">
       <label>Description of the sequence</label>
     </param>
     <param name="append" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_diffseq.xml
--- a/emboss_5/emboss_diffseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_diffseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -10,7 +10,7 @@
     <param format="data" name="input2" type="data">
       <label>Sequence 2</label>
     </param>
-    <param name="wordsize" size="4" type="text" value="20">
+    <param name="wordsize" type="text" value="20">
       <label>Wordsize</label>
     </param>
     <param name="globaldifferences" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_dotmatcher.xml
--- a/emboss_5/emboss_dotmatcher.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_dotmatcher.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -10,10 +10,10 @@
     <param format="data" name="input2" type="data">
       <label>Sequence 2</label>
     </param>
-    <param name="windowsize" size="4" type="text" value="10">
+    <param name="windowsize" type="text" value="10">
       <label>Window size</label>
     </param>
-    <param name="threshold" size="4" type="text" value="23">
+    <param name="threshold" type="text" value="23">
       <label>Threshold</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_dotpath.xml
--- a/emboss_5/emboss_dotpath.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_dotpath.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -10,7 +10,7 @@
     <param format="data" name="input2" type="data">
       <label>Sequence 2</label>
     </param>
-    <param name="wordsize" size="4" type="text" value="4">
+    <param name="wordsize" type="text" value="4">
       <label>Word size (Integer 2 or more)</label>
     </param>
     <param name="overlaps" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_dottup.xml
--- a/emboss_5/emboss_dottup.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_dottup.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -9,7 +9,7 @@
     <param format="data" name="input2" type="data">
       <label>Sequence 2</label>
     </param>
-    <param name="wordsize" size="4" type="text" value="4">
+    <param name="wordsize" type="text" value="4">
       <label>Word size</label>
     </param>
     <param name="boxit" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_dreg.xml
--- a/emboss_5/emboss_dreg.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_dreg.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequence 1</label>
     </param>
-    <param name="pattern" size="50" type="text" value="(AUG)">
+    <param name="pattern" type="text" value="(AUG)">
       <label>Regular expression pattern</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_einverted.xml
--- a/emboss_5/emboss_einverted.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_einverted.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,19 +6,19 @@
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
     </param>
-    <param name="gap" size="4" type="text" value="12">
+    <param name="gap" type="text" value="12">
       <label>Gap penalty</label>
     </param>
-    <param name="threshold" size="4" type="text" value="50">
+    <param name="threshold" type="text" value="50">
       <label>Minimum score threshold</label>
     </param>
-    <param name="match" size="4" type="text" value="3">
+    <param name="match" type="text" value="3">
       <label>Match score</label>
     </param>
-    <param name="mismatch" size="4" type="text" value="-4">
+    <param name="mismatch" type="text" value="-4">
       <label>Mismatch score</label>
     </param>
-    <param name="maxrepeat" size="4" type="text" value="2000">
+    <param name="maxrepeat" type="text" value="2000">
       <label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_epestfind.xml
--- a/emboss_5/emboss_epestfind.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_epestfind.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -7,7 +7,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="window" size="4" type="text" value="10">
+    <param name="window" type="text" value="10">
       <label>Minimal distance between positively charged amino acids</label>
     </param>
     <param name="order" type="select">
@@ -16,7 +16,7 @@
       <option value="1">Length</option>
       <option value="2">Position</option>
     </param>
-    <param name="threshold" size="4" type="text" value="5.0">
+    <param name="threshold" type="text" value="5.0">
       <label>Threshold value to discriminate weak from potential PEST motifs.</label>
     </param>
     <param name="potential" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_equicktandem.xml
--- a/emboss_5/emboss_equicktandem.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_equicktandem.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,10 +6,10 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="maxrepeat" size="4" type="text" value="600">
+    <param name="maxrepeat" type="text" value="600">
       <label>Maximum repeat size</label>
     </param>
-    <param name="threshold" size="4" type="text" value="20">
+    <param name="threshold" type="text" value="20">
       <label>Threshold score</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_est2genome.xml
--- a/emboss_5/emboss_est2genome.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_est2genome.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -10,22 +10,22 @@
     <param format="data" name="input2" type="data">
       <label>Genomic sequence</label>
     </param>
-    <param name="match" size="4" type="text" value="1">
+    <param name="match" type="text" value="1">
       <label>Score for matching two bases</label>
     </param>
-    <param name="mismatch" size="4" type="text" value="1">
+    <param name="mismatch" type="text" value="1">
       <label>Cost for mismatching two bases</label>
     </param>
-    <param name="gappenalty" size="4" type="text" value="2">
+    <param name="gappenalty" type="text" value="2">
       <label>Cost for deleting a single base in either sequence, excluding introns</label>
     </param>
-    <param name="intronpenalty" size="4" type="text" value="40">
+    <param name="intronpenalty" type="text" value="40">
       <label>Cost for an intron, independent of length</label>
     </param>
-    <param name="splicepenalty" size="4" type="text" value="20">
+    <param name="splicepenalty" type="text" value="20">
       <label>Cost for an intron, independent of length and starting/ending on donor-acceptor sites</label>
     </param>
-    <param name="minscore" size="4" type="text" value="30">
+    <param name="minscore" type="text" value="30">
       <label>Exclude alignments with scores below this threshold score</label>
     </param>
     <param name="reverse" type="select">
@@ -49,10 +49,10 @@
       <option value="yes">Yes</option>
       <option value="no">No</option>
     </param>
-    <param name="shuffle" size="4" type="text" value="0">
+    <param name="shuffle" type="text" value="0">
       <label>Shuffle</label>
     </param>
-    <param name="seed" size="4" type="text" value="20825">
+    <param name="seed" type="text" value="20825">
       <label>Random number seed</label>
     </param>
     <param name="align" type="select">
@@ -60,7 +60,7 @@
       <option value="no">No</option>
       <option value="yes">Yes</option>
     </param>
-    <param name="width" size="4" type="text" value="50">
+    <param name="width" type="text" value="50">
       <label>Alignment width</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_etandem.xml
--- a/emboss_5/emboss_etandem.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_etandem.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,13 +6,13 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="minrepeat" size="4" type="text" value="10">
+    <param name="minrepeat" type="text" value="10">
       <label>Minimum repeat size</label>
     </param>
-    <param name="maxrepeat" size="4" type="text" value="10">
+    <param name="maxrepeat" type="text" value="10">
       <label>Maximum repeat size</label>
     </param>
-    <param name="threshold" size="4" type="text" value="20">
+    <param name="threshold" type="text" value="20">
       <label>Threshold score</label>
     </param>
     <param name="mismatch" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_extractfeat.xml
--- a/emboss_5/emboss_extractfeat.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_extractfeat.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -8,16 +8,16 @@
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="before" size="4" type="text" value="0">
+    <param name="before" type="text" value="0">
       <label>Number of bases or residues before the feature to include in the extracted sequence</label>
     </param>
-    <param name="after" size="4" type="text" value="0">
+    <param name="after" type="text" value="0">
       <label>Number of bases or residues after the feature to include in the extracted sequence</label>
     </param>
-    <param name="source" size="4" type="text" value="*">
+    <param name="source" type="text" value="*">
       <label>Feature source</label>
     </param>
-    <param name="type" size="4" type="text" value="*">
+    <param name="type" type="text" value="*">
       <label>Feature type</label>
     </param>
     <param name="sense" type="select">
@@ -26,16 +26,16 @@
       <option value="1">Forward sense</option>
       <option value="-1">Reverse sense</option>
     </param>
-    <param name="minscore" size="4" type="text" value="0.0">
+    <param name="minscore" type="text" value="0.0">
       <label>Minimum score</label>
     </param>
-    <param name="maxscore" size="4" type="text" value="0.0">
+    <param name="maxscore" type="text" value="0.0">
       <label>Maximum score</label>
     </param>
-    <param name="tag" size="4" type="text" value="*">
+    <param name="tag" type="text" value="*">
       <label>Feature tags</label>
     </param>
-    <param name="value" size="4" type="text" value="*">
+    <param name="value" type="text" value="*">
       <label>Tag values</label>
     </param>
     <param name="join" type="select">
@@ -48,7 +48,7 @@
       <option value="no">No</option>
       <option value="yes">Yes</option>
     </param>
-    <param name="describe" size="4" type="text" value="">
+    <param name="describe" type="text" value="">
       <label>Specify one or more tag names that should be added to the output sequence Description text</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_extractseq.xml
--- a/emboss_5/emboss_extractseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_extractseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="regions" size="20" type="text" value="1-9999999">
+    <param name="regions" type="text" value="1-9999999">
       <label>Regions to extract</label>
     </param>
     <param name="separate" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_freak.xml
--- a/emboss_5/emboss_freak.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_freak.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,13 +6,13 @@
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="letters" size="5" type="text" value="gc">
+    <param name="letters" type="text" value="gc">
       <label>Residue letters</label>
     </param>
-    <param name="step" size="5" type="text" value="1">
+    <param name="step" type="text" value="1">
       <label>Stepping value</label>
     </param>
-    <param name="window" size="5" type="text" value="30">
+    <param name="window" type="text" value="30">
       <label>Averaging window</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_fuzznuc.xml
--- a/emboss_5/emboss_fuzznuc.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_fuzznuc.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="pattern" size="5" type="text" value="">
+    <param name="pattern" type="text" value="">
       <label>Search pattern</label>
       <sanitizer>
         <valid initial="string.printable">
@@ -17,7 +17,7 @@
         </mapping>
       </sanitizer>
     </param>
-    <param name="mismatch" size="5" type="text" value="0">
+    <param name="mismatch" type="text" value="0">
       <label>Number of mismatches</label>
     </param>
     <param name="complement" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_fuzzpro.xml
--- a/emboss_5/emboss_fuzzpro.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_fuzzpro.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,10 +6,10 @@
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="pattern" size="30" type="text" value="">
+    <param name="pattern" type="text" value="">
       <label>Search pattern</label>
     </param>
-    <param name="mismatch" size="5" type="text" value="0">
+    <param name="mismatch" type="text" value="0">
       <label>Number of mismatches</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_fuzztran.xml
--- a/emboss_5/emboss_fuzztran.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_fuzztran.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,10 +6,10 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="pattern" size="5" type="text" value="">
+    <param name="pattern" type="text" value="">
       <label>Search pattern</label>
     </param>
-    <param name="mismatch" size="5" type="text" value="0">
+    <param name="mismatch" type="text" value="0">
       <label>Number of mismatches</label>
     </param>
     <param name="frame" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_getorf.xml
--- a/emboss_5/emboss_getorf.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_getorf.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -28,10 +28,10 @@
       <option value="22">Scenedesmus obliquus</option>
       <option value="23">Thraustochytrium Mitochondrial</option>
     </param>
-    <param name="minsize" size="10" type="text" value="30">
+    <param name="minsize" type="text" value="30">
       <label>Minimum nucleotide size of ORF to report</label>
     </param>
-    <param name="maxsize" size="10" type="text" value="1000000">
+    <param name="maxsize" type="text" value="1000000">
       <label>Maximum nucleotide size of ORF to report</label>
     </param>
     <param name="find" type="select">
@@ -59,7 +59,7 @@
       <option value="yes">Yes</option>
       <option value="no">No</option>
     </param>
-    <param name="flanking" size="10" type="text" value="100">
+    <param name="flanking" type="text" value="100">
       <label>Number of flanking nucleotides to output</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_helixturnhelix.xml
--- a/emboss_5/emboss_helixturnhelix.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_helixturnhelix.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,13 +6,13 @@
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="mean" size="10" type="text" value="238.71">
+    <param name="mean" type="text" value="238.71">
       <label>Mean value</label>
     </param>
-    <param name="sd" size="10" type="text" value="293.61">
+    <param name="sd" type="text" value="293.61">
       <label>Standard Deviation value</label>
     </param>
-    <param name="minsd" size="10" type="text" value="2.5">
+    <param name="minsd" type="text" value="2.5">
       <label>Minimum SD</label>
     </param>
     <param name="eightyseven" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_hmoment.xml
--- a/emboss_5/emboss_hmoment.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_hmoment.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,10 +6,10 @@
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="window" size="5" type="text" value="10">
+    <param name="window" type="text" value="10">
       <label>Window</label>
     </param>
-    <param name="aangle" size="5" type="text" value="100">
+    <param name="aangle" type="text" value="100">
       <label>Alpha helix angle (degrees)</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_iep.xml
--- a/emboss_5/emboss_iep.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_iep.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,10 +6,10 @@
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="step" size="5" type="text" value=".5">
+    <param name="step" type="text" value=".5">
       <label>Step value for pH</label>
     </param>
-    <param name="amino" size="5" type="text" value="1">
+    <param name="amino" type="text" value="1">
       <label>Number of N-termini</label>
     </param>
     <param name="termini" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_isochore.xml
--- a/emboss_5/emboss_isochore.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_isochore.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -7,10 +7,10 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="window" size="4" type="text" value="1000">
+    <param name="window" type="text" value="1000">
       <label>Window size</label>
     </param>
-    <param name="shift" size="4" type="text" value="100">
+    <param name="shift" type="text" value="100">
       <label>Shift increment</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_lindna.xml
--- a/emboss_5/emboss_lindna.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_lindna.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -20,10 +20,10 @@
       <option value="Open">Open blocks</option>
       <option value="Outline">Black border</option>
     </param>
-    <param name="maxgroups" size="4" type="text" value="20">
+    <param name="maxgroups" type="text" value="20">
       <label>Maximum number of groups</label>
     </param>
-    <param name="maxlabels" size="6" type="text" value="10000">
+    <param name="maxlabels" type="text" value="10000">
       <label>Maximum number of labels</label>
     </param>
     <param name="intersymbol" type="select">
@@ -54,7 +54,7 @@
       <option value="no">No</option>
       <option value="yes">Yes</option>
     </param>
-    <param name="gapsize" size="6" type="text" value="500">
+    <param name="gapsize" type="text" value="500">
       <label>Interval between ticks in the ruler</label>
     </param>
     <param name="ticklines" type="select">
@@ -62,29 +62,29 @@
       <option value="no">No</option>
       <option value="yes">Yes</option>
     </param>
-    <param name="textheight" size="4" type="text" value="1.0">
+    <param name="textheight" type="text" value="1.0">
       <label>Height of text. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
     </param>
-    <param name="textlength" size="4" type="text" value="1.0">
+    <param name="textlength" type="text" value="1.0">
       <label>Length of text. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
     </param>
-    <param name="margin" size="4" type="text" value="1.0">
+    <param name="margin" type="text" value="1.0">
       <label>Width of left margin. This is the region left to the groups where the names of the groups are displayed. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size,
       respectively</label>
     </param>
-    <param name="tickheight" size="4" type="text" value="1.0">
+    <param name="tickheight" type="text" value="1.0">
       <label>Height of ticks. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
     </param>
-    <param name="blockheight" size="4" type="text" value="1.0">
+    <param name="blockheight" type="text" value="1.0">
       <label>Height of blocks. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
     </param>
-    <param name="rangeheight" size="4" type="text" value="1.0">
+    <param name="rangeheight" type="text" value="1.0">
       <label>Height of range ends. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
     </param>
-    <param name="gapgroup" size="4" type="text" value="1.0">
+    <param name="gapgroup" type="text" value="1.0">
       <label>Space between groups. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
     </param>
-    <param name="postext" size="4" type="text" value="1.0">
+    <param name="postext" type="text" value="1.0">
       <label>Space between text and ticks, blocks, and ranges. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_maskfeat.xml
--- a/emboss_5/emboss_maskfeat.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_maskfeat.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="type" size="50" type="text" value="repeat*">
+    <param name="type" type="text" value="repeat*">
       <label>Feature to mask</label>
     </param>
     <param name="tolower" type="select">
@@ -14,7 +14,7 @@
       <option value="no">No</option>
       <option value="yes">Yes</option>
     </param>
-    <param name="maskchar" size="1" type="text" value="N">
+    <param name="maskchar" type="text" value="N">
       <label>Character to mask with</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_maskseq.xml
--- a/emboss_5/emboss_maskseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_maskseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="regions" size="50" type="text" value="">
+    <param name="regions" type="text" value="">
       <label>Regions to mask (Example 1-99)</label>
     </param>
     <param name="tolower" type="select">
@@ -14,7 +14,7 @@
       <option value="no">No</option>
       <option value="yes">Yes</option>
     </param>
-    <param name="maskchar" size="1" type="text" value="N">
+    <param name="maskchar" type="text" value="N">
       <label>Character to use when masking</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_matcher.xml
--- a/emboss_5/emboss_matcher.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_matcher.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -9,13 +9,13 @@
     <param format="data" name="input2" type="data">
       <label>Sequence 2</label>
     </param>
-    <param name="alternatives" size="4" type="text" value="1">
+    <param name="alternatives" type="text" value="1">
       <label>Number of alternative matches</label>
     </param>
-    <param name="gapopen" size="4" type="text" value="16">
+    <param name="gapopen" type="text" value="16">
       <label>Gap penalty</label>
     </param>
-    <param name="gapextend" size="4" type="text" value="4">
+    <param name="gapextend" type="text" value="4">
       <label>Gap length (extension) penalty</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_megamerger.xml
--- a/emboss_5/emboss_megamerger.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_megamerger.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -9,7 +9,7 @@
     <param format="data" name="input2" type="data">
       <label>Sequence 2</label>
     </param>
-    <param name="wordsize" size="4" type="text" value="20">
+    <param name="wordsize" type="text" value="20">
       <label>Word size</label>
     </param>
     <param name="prefer" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_merger.xml
--- a/emboss_5/emboss_merger.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_merger.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -9,10 +9,10 @@
     <param format="data" name="input2" type="data">
       <label>Sequence 2</label>
     </param>
-    <param name="gapopen" size="4" type="text" value="50.0">
+    <param name="gapopen" type="text" value="50.0">
       <label>Gap opening penalty</label>
     </param>
-    <param name="gapextend" size="4" type="text" value="5.0">
+    <param name="gapextend" type="text" value="5.0">
       <label>Gap extension penalty</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_msbar.xml
--- a/emboss_5/emboss_msbar.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_msbar.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -7,7 +7,7 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequence 1</label>
     </param>
-    <param name="count" size="4" type="text" value="1">
+    <param name="count" type="text" value="1">
       <label>Number of times to perform the mutation operations</label>
     </param>
     <param name="point" type="select">
@@ -45,10 +45,10 @@
       <option value="no">No</option>
       <option value="yes">Yes</option>
     </param>
-    <param name="minimum" size="4" type="text" value="1">
+    <param name="minimum" type="text" value="1">
       <label>Minimum size for a block mutation</label>
     </param>
-    <param name="maximum" size="4" type="text" value="10">
+    <param name="maximum" type="text" value="10">
       <label>Maximum size for a block mutation</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_needle.xml
--- a/emboss_5/emboss_needle.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_needle.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -9,10 +9,10 @@
     <param format="fasta" name="input2" type="data">
       <label>Sequence 2</label>
     </param>
-    <param name="gapopen" size="4" type="text" value="10.0">
+    <param name="gapopen" type="text" value="10.0">
       <label>Gap open penalty</label>
     </param>
-    <param name="gapextend" size="4" type="text" value="0.5">
+    <param name="gapextend" type="text" value="0.5">
       <label>Gap extension penalty</label>
     </param>
     <param name="brief" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_newcpgreport.xml
--- a/emboss_5/emboss_newcpgreport.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_newcpgreport.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,19 +6,19 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="window" size="4" type="text" value="100">
+    <param name="window" type="text" value="100">
       <label>Window Size</label>
     </param>
-    <param name="shift" size="4" type="text" value="1">
+    <param name="shift" type="text" value="1">
       <label>Step size (shift)</label>
     </param>
-    <param name="minlen" size="4" type="text" value="200">
+    <param name="minlen" type="text" value="200">
       <label>Minimum length</label>
     </param>
-    <param name="minoe" size="4" type="text" value="0.6">
+    <param name="minoe" type="text" value="0.6">
       <label>Minimum average observed to expected ratio</label>
     </param>
-    <param name="minpc" size="4" type="text" value="50.0">
+    <param name="minpc" type="text" value="50.0">
       <label>Minimum average percentage of G plus C</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_newcpgseek.xml
--- a/emboss_5/emboss_newcpgseek.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_newcpgseek.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="score" size="4" type="text" value="17">
+    <param name="score" type="text" value="17">
       <label>CpG score</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_newseq.xml
--- a/emboss_5/emboss_newseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_newseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -3,10 +3,10 @@
   <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="">
+    <param name="seqname" type="text" value="">
       <label>Name of of the sequence</label>
     </param>
-    <param name="description" size="10" type="text" value="">
+    <param name="description" type="text" value="">
       <label>Description of the sequence</label>
     </param>
     <param name="type" type="select">
@@ -14,7 +14,7 @@
       <option value="N">Nucleic</option>
       <option value="P">Protein</option>
     </param>
-    <param name="sequence" size="50" type="text" value="">
+    <param name="sequence" type="text" value="">
       <label>The sequence itself</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_notseq.xml
--- a/emboss_5/emboss_notseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_notseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="fasta" name="input1" type="data">
       <label>On query</label>
     </param>
-    <param name="exclude" size="50" type="text" value="">
+    <param name="exclude" type="text" value="">
       <label>Exclude list</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_nthseq.xml
--- a/emboss_5/emboss_nthseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_nthseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="number" size="4" type="text" value="1">
+    <param name="number" type="text" value="1">
       <label>Number of the sequence to output</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_octanol.xml
--- a/emboss_5/emboss_octanol.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_octanol.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -8,7 +8,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="width" size="4" type="text" value="19">
+    <param name="width" type="text" value="19">
       <label>Window size</label>
     </param>
     <param name="octanolplot" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_oddcomp.xml
--- a/emboss_5/emboss_oddcomp.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_oddcomp.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -10,7 +10,7 @@
     <param format="data" name="input2" type="data">
       <label>This is a file in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis</label>
     </param>
-    <param name="window" size="4" type="text" value="30">
+    <param name="window" type="text" value="30">
       <label>This is the size of window in which to count. Thus if you want to count frequencies in a 40 aa stretch you should enter 40 here</label>
     </param>
     <param name="ignorebz" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_palindrome.xml
--- a/emboss_5/emboss_palindrome.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_palindrome.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,16 +6,16 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="minpallen" size="4" type="text" value="10">
+    <param name="minpallen" type="text" value="10">
       <label>Minimum length of palindrome</label>
     </param>
-    <param name="maxpallen" size="4" type="text" value="100">
+    <param name="maxpallen" type="text" value="100">
       <label>Maximum length of palindrome</label>
     </param>
-    <param name="gaplimit" size="4" type="text" value="100">
+    <param name="gaplimit" type="text" value="100">
       <label>Maximum gap between repeated regions</label>
     </param>
-    <param name="nummismatches" size="4" type="text" value="0">
+    <param name="nummismatches" type="text" value="0">
       <label>Number of mismatches allowed</label>
     </param>
     <param name="overlap" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_pasteseq.xml
--- a/emboss_5/emboss_pasteseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_pasteseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -9,7 +9,7 @@
     <param format="fasta" name="input2" type="data">
       <label>Sequence to insert</label>
     </param>
-    <param name="pos" size="4" type="text" value="0">
+    <param name="pos" type="text" value="0">
       <label>Position to insert after</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_patmatdb.xml
--- a/emboss_5/emboss_patmatdb.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_patmatdb.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="data" name="input1" type="data">
       <label>Main sequence</label>
     </param>
-    <param name="motif" size="4" type="text" value="">
+    <param name="motif" type="text" value="">
       <label>Motif to search for</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_pepcoil.xml
--- a/emboss_5/emboss_pepcoil.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_pepcoil.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="window" size="4" type="text" value="28">
+    <param name="window" type="text" value="28">
       <label>Window size</label>
     </param>
     <param name="coil" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_pepinfo.xml
--- a/emboss_5/emboss_pepinfo.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_pepinfo.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -7,7 +7,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="hwindow" size="4" type="text" value="9">
+    <param name="hwindow" type="text" value="9">
       <label>Window size for hydropathy averaging</label>
     </param>
     <param name="plot_type" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_pepnet.xml
--- a/emboss_5/emboss_pepnet.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_pepnet.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -7,13 +7,13 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="squares" size="10" type="text" value="ILVM">
+    <param name="squares" type="text" value="ILVM">
       <label>Residues to mark with squares</label>
     </param>
-    <param name="diamonds" size="10" type="text" value="DENQST">
+    <param name="diamonds" type="text" value="DENQST">
       <label>Residues to mark with diamonds</label>
     </param>
-    <param name="octags" size="10" type="text" value="HKR ">
+    <param name="octags" type="text" value="HKR ">
       <label>Residues to mark with octagons</label>
     </param>
     <param name="amphipathic" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_pepwheel.xml
--- a/emboss_5/emboss_pepwheel.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_pepwheel.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -8,19 +8,19 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="steps" size="10" type="text" value="18">
+    <param name="steps" type="text" value="18">
       <label>Steps, the number of residues plotted per turn is this value divided by the 'turns' value</label>
     </param>
-    <param name="turns" size="10" type="text" value="5">
+    <param name="turns" type="text" value="5">
       <label>Turns, the number of residues plotted per turn is the 'steps' value divided by this value</label>
     </param>
-    <param name="squares" size="10" type="text" value="ILVM">
+    <param name="squares" type="text" value="ILVM">
       <label>Residues to mark with squares</label>
     </param>
-    <param name="diamonds" size="10" type="text" value="DENQST">
+    <param name="diamonds" type="text" value="DENQST">
       <label>Residues to mark with diamonds</label>
     </param>
-    <param name="octags" size="10" type="text" value="HKR">
+    <param name="octags" type="text" value="HKR">
       <label>Residues to mark with octagons</label>
     </param>
     <param name="wheel" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_pepwindow.xml
--- a/emboss_5/emboss_pepwindow.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_pepwindow.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -7,7 +7,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="length" size="10" type="text" value="7">
+    <param name="length" type="text" value="7">
       <label>Window size</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_pepwindowall.xml
--- a/emboss_5/emboss_pepwindowall.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_pepwindowall.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -7,7 +7,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="length" size="10" type="text" value="7">
+    <param name="length" type="text" value="7">
       <label>Window size</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_plotcon.xml
--- a/emboss_5/emboss_plotcon.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_plotcon.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -7,7 +7,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="winsize" size="10" type="text" value="4">
+    <param name="winsize" type="text" value="4">
       <label>Number of columns to average alignment quality over</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_plotorf.xml
--- a/emboss_5/emboss_plotorf.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_plotorf.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -7,10 +7,10 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="start" size="15" type="text" value="ATG">
+    <param name="start" type="text" value="ATG">
       <label>Start codons</label>
     </param>
-    <param name="stop" size="15" type="text" value="TAA">
+    <param name="stop" type="text" value="TAA">
       <label>Stop codons</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_polydot.xml
--- a/emboss_5/emboss_polydot.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_polydot.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -8,7 +8,7 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="wordsize" size="10" type="text" value="6">
+    <param name="wordsize" type="text" value="6">
       <label>Word size</label>
     </param>
     <param name="boxit" type="select">
@@ -16,7 +16,7 @@
       <option value="yes">Yes</option>
       <option value="no">No</option>
     </param>
-    <param name="gap" size="10" type="text" value="10">
+    <param name="gap" type="text" value="10">
       <label>Size of gap</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_preg.xml
--- a/emboss_5/emboss_preg.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_preg.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequence 1</label>
     </param>
-    <param name="pattern" size="50" type="text" value="(ACD)">
+    <param name="pattern" type="text" value="(ACD)">
       <label>Regular expression pattern</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_prettyplot.xml
--- a/emboss_5/emboss_prettyplot.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_prettyplot.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -9,10 +9,10 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="residuesperline" size="10" type="text" value="50">
+    <param name="residuesperline" type="text" value="50">
       <label>The number of residues to be displayed on each line</label>
     </param>
-    <param name="resbreak" size="10" type="text" value="50">
+    <param name="resbreak" type="text" value="50">
       <label>Residues before a space</label>
     </param>
     <param name="ccolours" type="select">
@@ -20,13 +20,13 @@
       <option value="yes">Yes</option>
       <option value="no">No</option>
     </param>
-    <param name="cidentity" size="10" type="text" value="RED">
+    <param name="cidentity" type="text" value="RED">
       <label>Colour to display identical residues</label>
     </param>
-    <param name="csimilarity" size="10" type="text" value="GREEN">
+    <param name="csimilarity" type="text" value="GREEN">
       <label>Colour to display similar residues</label>
     </param>
-    <param name="cother" size="10" type="text" value="BLACK">
+    <param name="cother" type="text" value="BLACK">
       <label>Colour to display other residues</label>
     </param>
     <param name="docolour" type="select">
@@ -39,10 +39,10 @@
       <option value="yes">Yes</option>
       <option value="no">No</option>
     </param>
-    <param name="pair" size="10" type="text" value="1.5,1.0,0.5">
+    <param name="pair" type="text" value="1.5,1.0,0.5">
       <label>Values to represent identical similar related</label>
     </param>
-    <param name="identity" size="10" type="text" value="0">
+    <param name="identity" type="text" value="0">
       <label>Only match those which are identical in all sequences</label>
     </param>
     <param name="box" type="select">
@@ -55,7 +55,7 @@
       <option value="no">No</option>
       <option value="yes">Yes</option>
     </param>
-    <param name="boxcolval" size="10" type="text" value="GREY">
+    <param name="boxcolval" type="text" value="GREY">
       <label>Colour to be used for background</label>
     </param>
     <param name="name" type="select">
@@ -63,7 +63,7 @@
       <option value="yes">Yes</option>
       <option value="no">No</option>
     </param>
-    <param name="maxnamelen" size="10" type="text" value="10">
+    <param name="maxnamelen" type="text" value="10">
       <label>Margin size for the sequence name</label>
     </param>
     <param name="number" type="select">
@@ -93,7 +93,7 @@
       <option value="2">If another residue has a greater than or equal to matching score and these do not match then a collision has occurred</option>
       <option value="3">Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured</option>
     </param>
-    <param name="showscore" size="10" type="text" value="-1">
+    <param name="showscore" type="text" value="-1">
       <label>Print residue scores</label>
     </param>
     <param name="portrait" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_prettyseq.xml
--- a/emboss_5/emboss_prettyseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_prettyseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -21,7 +21,7 @@
       <option value="yes">Yes</option>
       <option value="no">No</option>
     </param>
-    <param name="width" size="4" type="text" value="60">
+    <param name="width" type="text" value="60">
       <label>Width of screen</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_primersearch.xml
--- a/emboss_5/emboss_primersearch.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_primersearch.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -9,7 +9,7 @@
     <param format="data" name="input2" type="data">
       <label>Primer file</label>
     </param>
-    <param name="mismatchpercent" size="4" type="text" value="0">
+    <param name="mismatchpercent" type="text" value="0">
       <label>Allowed percent mismatch</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_seqmatchall.xml
--- a/emboss_5/emboss_seqmatchall.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_seqmatchall.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="wordsize" size="4" type="text" value="4">
+    <param name="wordsize" type="text" value="4">
       <label>Word size</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_showfeat.xml
--- a/emboss_5/emboss_showfeat.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_showfeat.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -14,16 +14,16 @@
       <option value="no">No</option>
       <option value="yes">Yes</option>
     </param>
-    <param name="matchsource" size="50" type="text" value="*">
+    <param name="matchsource" type="text" value="*">
       <label>Feature source to match</label>
     </param>
-    <param name="matchtype" size="50" type="text" value="*">
+    <param name="matchtype" type="text" value="*">
       <label>Feature type to match</label>
     </param>
-    <param name="matchtag" size="50" type="text" value="*">
+    <param name="matchtag" type="text" value="*">
       <label>Feature tags to match</label>
     </param>
-    <param name="matchvalue" size="50" type="text" value="*">
+    <param name="matchvalue" type="text" value="*">
       <label>Tag values to match</label>
     </param>
     <param name="sort" type="select">
@@ -34,7 +34,7 @@
       <option value="nosort">No sorting done</option>
       <option value="join">Join coding regions together</option>
     </param>
-    <param name="annotation" size="50" type="text" value="">
+    <param name="annotation" type="text" value="">
       <label>Regions to annotate by marking</label>
     </param>
     <param name="id" type="select">
@@ -52,7 +52,7 @@
       <option value="yes">Yes</option>
       <option value="no">No</option>
     </param>
-    <param name="width" size="50" type="text" value="60">
+    <param name="width" type="text" value="60">
       <label>Screen width</label>
     </param>
     <param name="collapse" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_shuffleseq.xml
--- a/emboss_5/emboss_shuffleseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_shuffleseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -7,7 +7,7 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="shuffle" size="4" type="text" value="1">
+    <param name="shuffle" type="text" value="1">
       <label>Number of shuffles</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_sigcleave.xml
--- a/emboss_5/emboss_sigcleave.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_sigcleave.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="minweight" size="4" type="text" value="3.5">
+    <param name="minweight" type="text" value="3.5">
       <label>Minimum scoring weight value for the predicted cleavage site</label>
     </param>
     <param name="prokaryote" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_sixpack.xml
--- a/emboss_5/emboss_sixpack.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_sixpack.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -49,10 +49,10 @@
       <option value="yes">Yes</option>
       <option value="no">No</option>
     </param>
-    <param name="orfminsize" size="4" type="text" value="1">
+    <param name="orfminsize" type="text" value="1">
       <label>Minimum size of Open Reading Frames (ORFs) to display in the translations</label>
     </param>
-    <param name="uppercase" size="50" type="text" value="">
+    <param name="uppercase" type="text" value="">
       <label>Regions to put in uppercase</label>
     </param>
     <param name="number" type="select">
@@ -60,13 +60,13 @@
       <option value="yes">Yes</option>
       <option value="no">No</option>
     </param>
-    <param name="width" size="4" type="text" value="60">
+    <param name="width" type="text" value="60">
       <label>Number of nucleotides displayed on each line</label>
     </param>
-    <param name="length" size="4" type="text" value="0">
+    <param name="length" type="text" value="0">
       <label>Line length of page</label>
     </param>
-    <param name="margin" size="4" type="text" value="10">
+    <param name="margin" type="text" value="10">
       <label>Margin around sequence for numbering</label>
     </param>
     <param name="disp_name" type="select">
@@ -79,7 +79,7 @@
       <option value="yes">Yes</option>
       <option value="no">No</option>
     </param>
-    <param name="offset" size="4" type="text" value="1">
+    <param name="offset" type="text" value="1">
       <label>Number from which you want the DNA sequence to be numbered</label>
     </param>
     <param name="html_out1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_skipseq.xml
--- a/emboss_5/emboss_skipseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_skipseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="skip" size="4" type="text" value="0">
+    <param name="skip" type="text" value="0">
       <label>Number of sequences to skip at start</label>
     </param>
     <param name="feature" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_splitter.xml
--- a/emboss_5/emboss_splitter.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_splitter.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,10 +6,10 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="size" size="10" type="text" value="10000">
+    <param name="size" type="text" value="10000">
       <label>Size to split at</label>
     </param>
-    <param name="overlap" size="4" type="text" value="0">
+    <param name="overlap" type="text" value="0">
       <label>Overlap between split sequences</label>
     </param>
     <param name="addoverlap" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_supermatcher.xml
--- a/emboss_5/emboss_supermatcher.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_supermatcher.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -11,16 +11,16 @@
     <param format="data" name="input2" type="data">
       <label>Sequences to match</label>
     </param>
-    <param name="gapopen" size="4" type="text" value="10.0">
+    <param name="gapopen" type="text" value="10.0">
       <label>Gap opening penalty</label>
     </param>
-    <param name="gapextend" size="4" type="text" value="0.5">
+    <param name="gapextend" type="text" value="0.5">
       <label>Gap extension penalty</label>
     </param>
-    <param name="width" size="4" type="text" value="16">
+    <param name="width" type="text" value="16">
       <label>Alignment width</label>
     </param>
-    <param name="wordlen" size="4" type="text" value="6">
+    <param name="wordlen" type="text" value="6">
       <label>Word length for initial matching</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_syco.xml
--- a/emboss_5/emboss_syco.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_syco.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -162,7 +162,7 @@
       <option value="Ezebrafish.cut">Ezebrafish.cut</option>
       <option value="Ezma.cut">Ezma.cut</option>
     </param>
-    <param name="window" size="4" type="text" value="30">
+    <param name="window" type="text" value="30">
       <label>Averaging window</label>
     </param>
     <param name="uncommon" type="select">
@@ -170,7 +170,7 @@
       <option value="no">No</option>
       <option value="yes">Yes</option>
     </param>
-    <param name="minimum" size="4" type="text" value="0.15">
+    <param name="minimum" type="text" value="0.15">
       <label>Minimum value for a common codon</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_tcode.xml
--- a/emboss_5/emboss_tcode.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_tcode.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,10 +6,10 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="window" size="5" type="text" value="200">
+    <param name="window" type="text" value="200">
       <label>Window size</label>
     </param>
-    <param name="step" size="5" type="text" value="3">
+    <param name="step" type="text" value="3">
       <label>Step size</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_textsearch.xml
--- a/emboss_5/emboss_textsearch.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_textsearch.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -7,7 +7,7 @@
     <param format="data" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="pattern" size="50" type="text" value="">
+    <param name="pattern" type="text" value="">
       <label>Pattern to search for</label>
     </param>
     <param name="casesensitive" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_transeq.xml
--- a/emboss_5/emboss_transeq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_transeq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -39,7 +39,7 @@
       <option value="22">Scenedesmus obliquus</option>
       <option value="23">Thraustochytrium Mitochondrial</option>
     </param>
-    <param name="regions" size="10" type="text" value="">
+    <param name="regions" type="text" value="">
       <label>Regions to translate</label>
     </param>
     <param name="trim" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_trimest.xml
--- a/emboss_5/emboss_trimest.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_trimest.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -7,10 +7,10 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="minlength" size="4" type="text" value="4">
+    <param name="minlength" type="text" value="4">
       <label>Minimum length that a poly-A (or poly-T) tail must have before it is removed</label>
     </param>
-    <param name="mismatches" size="4" type="text" value="1">
+    <param name="mismatches" type="text" value="1">
       <label>Number of fewer mismatched non-A bases in a poly-A tail</label>
     </param>
     <param name="reverse" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_trimseq.xml
--- a/emboss_5/emboss_trimseq.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_trimseq.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,10 +6,10 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="window" size="4" type="text" value="1">
+    <param name="window" type="text" value="1">
       <label>Window size</label>
     </param>
-    <param name="percent" size="5" type="text" value="100.0">
+    <param name="percent" type="text" value="100.0">
       <label>Threshold of the percentage ambiguity</label>
     </param>
     <param name="strict" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_twofeat.xml
--- a/emboss_5/emboss_twofeat.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_twofeat.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -8,19 +8,19 @@
     <param format="data" name="input1" type="data">
       <label>Sequences</label>
     </param>
-    <param name="atype" size="50" type="text" value="*">
+    <param name="atype" type="text" value="*">
       <label>Feature type you wish to allow. Feature 1</label>
     </param>
-    <param name="btype" size="50" type="text" value="*">
+    <param name="btype" type="text" value="*">
       <label>Feature type you wish to allow. Feature 2</label>
     </param>
-    <param name="minrange" size="5" type="text" value="0">
+    <param name="minrange" type="text" value="0">
       <label>Minimun range</label>
     </param>
-    <param name="maxrange" size="5" type="text" value="0">
+    <param name="maxrange" type="text" value="0">
       <label>Maximum range</label>
     </param>
-    <param name="asource" size="50" type="text" value="*">
+    <param name="asource" type="text" value="*">
       <label>Feature source 1</label>
     </param>
     <param name="asense" type="select">
@@ -29,19 +29,19 @@
       <option value="+">Forward sense</option>
       <option value="-">Reverse sense</option>
     </param>
-    <param name="aminscore" size="5" type="text" value="0.0">
+    <param name="aminscore" type="text" value="0.0">
       <label>Feature 1 minimum score</label>
     </param>
-    <param name="amaxscore" size="5" type="text" value="0.0">
+    <param name="amaxscore" type="text" value="0.0">
       <label>Feature1 maxiumum score</label>
     </param>
-    <param name="atag" size="50" type="text" value="*">
+    <param name="atag" type="text" value="*">
       <label>Feature 1 tag</label>
     </param>
-    <param name="avalue" size="50" type="text" value="*">
+    <param name="avalue" type="text" value="*">
       <label>Tag 1 value</label>
     </param>
-    <param name="bsource" size="50" type="text" value="*">
+    <param name="bsource" type="text" value="*">
       <label>Feature 2 source</label>
     </param>
     <param name="bsense" type="select">
@@ -50,16 +50,16 @@
       <option value="+">Forward sense</option>
       <option value="-">Reverse sense</option>
     </param>
-    <param name="bminscore" size="5" type="text" value="0.0">
+    <param name="bminscore" type="text" value="0.0">
       <label>Feature 2 miniumum score</label>
     </param>
-    <param name="bmaxscore" size="5" type="text" value="0.0">
+    <param name="bmaxscore" type="text" value="0.0">
       <label>Feature 2 maximum score</label>
     </param>
-    <param name="btag" size="50" type="text" value="*">
+    <param name="btag" type="text" value="*">
       <label>Feature 2 tag</label>
     </param>
-    <param name="bvalue" size="50" type="text" value="*">
+    <param name="bvalue" type="text" value="*">
       <label>Feature 2 tag value</label>
     </param>
     <param name="overlap" type="select">
@@ -95,7 +95,7 @@
       <option value="no">No</option>
       <option value="yes">Yes</option>
     </param>
-    <param name="typeout" size="50" type="text" value="misc_feature">
+    <param name="typeout" type="text" value="misc_feature">
       <label>New feature type</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_vectorstrip.xml
--- a/emboss_5/emboss_vectorstrip.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_vectorstrip.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -10,7 +10,7 @@
     <param format="data" name="input2" type="data">
       <label>Vector file</label>
     </param>
-    <param name="mismatch" size="4" type="text" value="10">
+    <param name="mismatch" type="text" value="10">
       <label>Max allowed percent mismatch</label>
     </param>
     <param name="besthits" type="select">
@@ -18,10 +18,10 @@
       <option value="yes">Yes</option>
       <option value="no">No</option>
     </param>
-    <param name="linkera" size="50" type="text" value="">
+    <param name="linkera" type="text" value="">
       <label>The 5' sequence</label>
     </param>
-    <param name="linkerb" size="50" type="text" value="">
+    <param name="linkerb" type="text" value="">
       <label>The 3' sequence</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_water.xml
--- a/emboss_5/emboss_water.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_water.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -9,10 +9,10 @@
     <param format="fasta" name="input2" type="data">
       <label>Sequence 2</label>
     </param>
-    <param name="gapopen" size="6" type="text" value="10.0">
+    <param name="gapopen" type="text" value="10.0">
       <label>Gap open penalty</label>
     </param>
-    <param name="gapextend" size="6" type="text" value="0.5">
+    <param name="gapextend" type="text" value="0.5">
       <label>Gap extension penalty</label>
     </param>
     <param name="brief" type="select">
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_wobble.xml
--- a/emboss_5/emboss_wobble.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_wobble.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,10 +6,10 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="window" size="5" type="text" value="30">
+    <param name="window" type="text" value="30">
       <label>Window size, in codons</label>
     </param>
-    <param name="bases" size="6" type="text" value="GC">
+    <param name="bases" type="text" value="GC">
       <label>Bases used</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_wordcount.xml
--- a/emboss_5/emboss_wordcount.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_wordcount.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -6,7 +6,7 @@
     <param format="fasta" name="input1" type="data">
       <label>Sequence</label>
     </param>
-    <param name="wordsize" size="5" type="text" value="4">
+    <param name="wordsize" type="text" value="4">
       <label>Word size</label>
     </param>
   </inputs>
diff -r ce22ceec214a -r b810c96613ee emboss_5/emboss_wordmatch.xml
--- a/emboss_5/emboss_wordmatch.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/emboss_5/emboss_wordmatch.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -10,7 +10,7 @@
     <param format="fasta" name="input2" type="data">
       <label>Sequence 2</label>
     </param>
-    <param name="wordsize" size="5" type="text" value="4">
+    <param name="wordsize" type="text" value="4">
       <label>Word size</label>
     </param>
     <param name="out_format1" type="select">
diff -r ce22ceec214a -r b810c96613ee repository_dependencies.xml
--- a/repository_dependencies.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/repository_dependencies.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="Emboss 5 requires the Galaxy applicable data formats used by Emboss tools.">
-    <repository toolshed="http://toolshed.g2.bx.psu.edu" name="emboss_datatypes" owner="devteam" changeset_revision="a89163f31369" />
-</repositories>
\ No newline at end of file
+    <repository changeset_revision="a89163f31369" name="emboss_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+</repositories>
diff -r ce22ceec214a -r b810c96613ee tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Dec 11 16:27:03 2013 -0500
+++ b/tool_dependencies.xml	Wed Nov 11 12:12:41 2015 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="emboss" version="5.0.0">
-        <repository changeset_revision="cf998ddc0542" name="package_emboss_5_0_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="cf998ddc0542" name="package_emboss_5_0_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>