Mercurial > repos > greg > meme_psp_gen
changeset 4:01d22cb1bccc draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 21 Aug 2017 08:16:59 -0400 |
| parents | 79df81990900 |
| children | e994f439190c |
| files | meme_psp_gen.xml |
| diffstat | 1 files changed, 12 insertions(+), 79 deletions(-) [+] |
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--- a/meme_psp_gen.xml Fri Aug 18 11:11:13 2017 -0400 +++ b/meme_psp_gen.xml Mon Aug 21 08:16:59 2017 -0400 @@ -11,35 +11,7 @@ -minw $adv.minw -maxw $adv.maxw $adv.alphabet -#if str($adv.triples_cond.triples) == 'yes': - -triples - #if str($adv.triples_cond.fixed_start) == 'yes': - -fixedstart - #end if -#end if -#if str($adv.equiv) == 'yes': - -equiv -#end if -#if str($adv.consider_both_strands) == 'yes': - -revcomp -#end if -#if str($adv.scale_min) == 'yes': - -scalemin -#end if -#if str($adv.scale_max) == 'yes': - -scalemax -#end if -#if str($adv.max_range) == 'yes': - -maxrange -#end if -#if str($adv.raw) == 'yes': - -raw -#end if -#if str($adv.report_scores_cond.report_scores) == 'yes': - -reportscores - #if str($adv.report_scores_cond.verbose) == 'yes': - -verbose - #end if +#if $adv.report_scores_cond.report_scores: 2> '$output_tabular' #end if > '$output_psp' @@ -56,53 +28,23 @@ <option value="-rna">RNA</option> </param> <conditional name="triples_cond"> - <param name="triples" type="select" label="Use spaced triples instead of whole-word matches?" help="Recommended for protein"> - <option value="no" selected="true">No</option> - <option value="yes">yes</option> - </param> + <param name="triples" type="boolean" truevalue="-triples" falsevalue="" checked="False" label="Use spaced triples instead of whole-word matches?" help="Recommended for protein"/> <when value="no"/> <when value="yes"> - <param name="fixed_start" type="select" display="radio" label="Allow triples to start anywhere within a site?" help="Select 'No' to only consider triples starting at the start of the site"> - <option value="yes" selected="true">Yes</option> - <option value="no">No</option> - </param> + <param name="fixed_start" type="boolean" truevalue="-fixedstart" falsevalue="" checked="False" label="Allow triples to start anywhere within a site?" help="Select 'No' to only consider triples starting at the start of the site"/> </when> </conditional> - <param name="equiv" type="select" display="radio" label="Match as equal sequences of letters that appear together?"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <param name="consider_both_strands" type="select" display="radio" label="Consider both strands when calculating position specific priors for alphabets?"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <param name="scale_min" type="select" display="radio" label="Set the lowest score value after scaling?"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <param name="scale_max" type="select" display="radio" label="Set the highest score value after scaling?"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <param name="max_range" type="select" display="radio" label="Choose the width with the biggest difference between minimum and maximum scores before scaling?" help="Select 'No' to choose the width with the biggest maximum score (before scaling)"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <param name="raw" type="select" display="radio" label="Output scores instead of priors?"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> + <param name="equiv" type="boolean" truevalue="-equiv" falsevalue="" checked="False" label="Match as equal sequences of letters that appear together?"/> + <param name="consider_both_strands" type="boolean" truevalue="-revcomp" falsevalue="" checked="False" label="Consider both strands when calculating position specific priors for alphabets?"/> + <param name="scale_min" type="boolean" truevalue="-scalemin" falsevalue="" checked="False" label="Set the lowest score value after scaling?"/> + <param name="scale_max" type="boolean" truevalue="-scalemax" falsevalue="" checked="False" label="Set the highest score value after scaling?"/> + <param name="max_range" type="boolean" truevalue="-maxrange" falsevalue="" checked="False" label="Choose the width with the biggest difference between minimum and maximum scores before scaling?" help="Select 'No' to choose the width with the biggest maximum score (before scaling)"/> + <param name="raw" type="boolean" truevalue="-raw" falsevalue="" checked="False" label="Output scores instead of priors?"/> <conditional name="report_scores_cond"> - <param name="report_scores" type="select" label="Output primary and control file names, scores and widths?"> - <option value="no" selected="true">No</option> - <option value="yes">yes</option> - </param> + <param name="report_scores" type="boolean" truevalue="-reportscores" falsevalue="" checked="False" label="Output primary and control file names, scores and widths?"/> <when value="no"/> <when value="yes"> - <param name="verbose" type="select" display="radio" label="Report frequency of each score?"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> + <param name="verbose" type="boolean" truevalue="-verbose" falsevalue="" checked="False" label="Report frequency of each score?"/> </when> </conditional> </section> @@ -172,15 +114,6 @@ </help> <citations> - <citation type="bibtex"> - @article{Bailey2010, - journal = {BMC Bioinformatics} - author = {Bailey Timothy L, Bodén Mikael, Whitington Tom, Machanick Philip}, - title = {The value of position-specific priors in motif discovery using MEME}, - year = {2010}, - volume = {11}, - number = {1}, - pages = {179} - }</citation> + <citation type="doi">10.1186/1471-2105-11-179</citation> </citations> </tool>