| Previous changeset 7:ce22ceec214a (2013-12-11) Next changeset 9:511429456d3c (2016-05-09) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7 |
|
modified:
emboss_5/emboss_antigenic.xml emboss_5/emboss_biosed.xml emboss_5/emboss_charge.xml emboss_5/emboss_checktrans.xml emboss_5/emboss_compseq.xml emboss_5/emboss_cpgplot.xml emboss_5/emboss_cpgreport.xml emboss_5/emboss_cutseq.xml emboss_5/emboss_dan.xml emboss_5/emboss_descseq.xml emboss_5/emboss_diffseq.xml emboss_5/emboss_dotmatcher.xml emboss_5/emboss_dotpath.xml emboss_5/emboss_dottup.xml emboss_5/emboss_dreg.xml emboss_5/emboss_einverted.xml emboss_5/emboss_epestfind.xml emboss_5/emboss_equicktandem.xml emboss_5/emboss_est2genome.xml emboss_5/emboss_etandem.xml emboss_5/emboss_extractfeat.xml emboss_5/emboss_extractseq.xml emboss_5/emboss_freak.xml emboss_5/emboss_fuzznuc.xml emboss_5/emboss_fuzzpro.xml emboss_5/emboss_fuzztran.xml emboss_5/emboss_getorf.xml emboss_5/emboss_helixturnhelix.xml emboss_5/emboss_hmoment.xml emboss_5/emboss_iep.xml emboss_5/emboss_isochore.xml emboss_5/emboss_lindna.xml emboss_5/emboss_maskfeat.xml emboss_5/emboss_maskseq.xml emboss_5/emboss_matcher.xml emboss_5/emboss_megamerger.xml emboss_5/emboss_merger.xml emboss_5/emboss_msbar.xml emboss_5/emboss_needle.xml emboss_5/emboss_newcpgreport.xml emboss_5/emboss_newcpgseek.xml emboss_5/emboss_newseq.xml emboss_5/emboss_notseq.xml emboss_5/emboss_nthseq.xml emboss_5/emboss_octanol.xml emboss_5/emboss_oddcomp.xml emboss_5/emboss_palindrome.xml emboss_5/emboss_pasteseq.xml emboss_5/emboss_patmatdb.xml emboss_5/emboss_pepcoil.xml emboss_5/emboss_pepinfo.xml emboss_5/emboss_pepnet.xml emboss_5/emboss_pepwheel.xml emboss_5/emboss_pepwindow.xml emboss_5/emboss_pepwindowall.xml emboss_5/emboss_plotcon.xml emboss_5/emboss_plotorf.xml emboss_5/emboss_polydot.xml emboss_5/emboss_preg.xml emboss_5/emboss_prettyplot.xml emboss_5/emboss_prettyseq.xml emboss_5/emboss_primersearch.xml emboss_5/emboss_seqmatchall.xml emboss_5/emboss_showfeat.xml emboss_5/emboss_shuffleseq.xml emboss_5/emboss_sigcleave.xml emboss_5/emboss_sixpack.xml emboss_5/emboss_skipseq.xml emboss_5/emboss_splitter.xml emboss_5/emboss_supermatcher.xml emboss_5/emboss_syco.xml emboss_5/emboss_tcode.xml emboss_5/emboss_textsearch.xml emboss_5/emboss_transeq.xml emboss_5/emboss_trimest.xml emboss_5/emboss_trimseq.xml emboss_5/emboss_twofeat.xml emboss_5/emboss_vectorstrip.xml emboss_5/emboss_water.xml emboss_5/emboss_wobble.xml emboss_5/emboss_wordcount.xml emboss_5/emboss_wordmatch.xml repository_dependencies.xml tool_dependencies.xml |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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 <1.0 or >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 <1.0 or >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 <1.0 or >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 <1.0 or >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 <1.0 or >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 <1.0 or >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 <1.0 or >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 <1.0 or >1.0 to decrease or increase the size, respectively</label> </param> </inputs> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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"> |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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 |
| b |
| @@ -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> |