Mercurial > repos > xuebing > sharplabtool
diff meme.xml @ 14:76e1b1b21cce default tip
Deleted selected files
author | xuebing |
---|---|
date | Tue, 13 Mar 2012 19:05:10 -0400 |
parents | 292186c14b08 |
children |
line wrap: on
line diff
--- a/meme.xml Sat Mar 10 08:17:36 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,349 +0,0 @@ -<tool id="meme_meme" name="MEME" version="1.0.0"> - <requirements><requirement type='package'>meme</requirement></requirements> - <description>motif discovery</description> - <command>meme "$input1" -o "${html_outfile.files_path}" - -nostatus - - ##-p 8 ##number of processors - - #if str( $options_type.options_type_selector ) == 'advanced': - -sf "${ str( $options_type.sf ).replace( ' ', '_' ) }" - -${options_type.alphabet_type.alphabet_type_selector} - -mod "${options_type.mod_type.mod_type_selector}" - -nmotifs "${options_type.nmotifs}" - -wnsites "${options_type.wnsites}" - -maxsize "${options_type.maxsize}" - - #if $options_type.evt < float('inf'): - -evt "${options_type.evt}" - #end if - - #if str( $options_type.mod_type.mod_type_selector ) != 'oops': - #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites': - -nsites "${options_type.mod_type.motif_occurrence_type.nsites}" - #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites': - -minsites "${options_type.mod_type.motif_occurrence_type.minsites}" -maxsites "${options_type.mod_type.motif_occurrence_type.maxsites}" - #end if - #end if - - #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact': - -w "${options_type.motif_width_type.width}" - #else - -minw "${options_type.motif_width_type.minw}" -maxw "${options_type.motif_width_type.maxw}" - #end if - - #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim': - -nomatrim - #else - -wg "${options_type.motif_trim_type.wg}" -ws "${options_type.motif_trim_type.ws}" ${options_type.motif_trim_type.noendgaps} - #end if - - #if str( $options_type.bfile ) != 'None': - -bfile "${options_type.bfile}" - #end if - - #if str( $options_type.pspfile ) != 'None': - -psp "${options_type.pspfile}" - #end if - - #if str( $options_type.alphabet_type.alphabet_type_selector ) == "dna": - ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal} - #end if - - -maxiter "${options_type.maxiter}" -distance "${options_type.distance}" - - -prior "${options_type.alphabet_type.prior_type.prior_type_selector}" - #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone': - -b "${options_type.alphabet_type.prior_type.prior_b}" - #if str( $options_type.alphabet_type.prior_type.plib ) != 'None': - -plib "${options_type.alphabet_type.prior_type.plib}" - #end if - #end if - - #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons': - -cons "${options_type.alphabet_type.spmap_type.cons}" - #else - -spmap "${options_type.alphabet_type.spmap_type.spmap_type_selector}" - -spfuzz "${options_type.alphabet_type.spmap_type.spfuzz}" - #end if - - #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch': - -x_branch -bfactor "${options_type.branching_type.bfactor}" -heapsize "${options_type.branching_type.heapsize}" - #end if - - ##-maxsize "1000000" ##remove hardcoded maxsize? should increase number of processors instead - - #end if - - 2>&1 || echo "Error running MEME." - - - && mv ${html_outfile.files_path}/meme.html ${html_outfile} - - && mv ${html_outfile.files_path}/meme.txt ${txt_outfile} - - && mv ${html_outfile.files_path}/meme.xml ${xml_outfile} - - </command> - <inputs> - <param format="fasta" name="input1" type="data" label="Sequences"/> - - <conditional name="options_type"> - <param name="options_type_selector" type="select" label="Options Configuration"> - <option value="basic" selected="true">Basic</option> - <option value="advanced">Advanced</option> - </param> - <when value="basic"> - <!-- do nothing here --> - </when> - <when value="advanced"> - - <param name="sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set" /> - - <conditional name="alphabet_type"> - <param name="alphabet_type_selector" type="select" label="Sequence Alphabet"> - <option value="protein">Protein</option> - <option value="dna" selected="true">DNA</option> - </param> - <when value="protein"> - <conditional name="prior_type"> - <param name="prior_type_selector" type="select" label="Choice of prior"> - <option value="dirichlet">simple Dirichlet prior</option> - <option value="dmix" selected="true">mixture of Dirichlets prior</option> - <option value="mega">extremely low variance dmix</option> - <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option> - <option value="addone">add +1 to each observed count</option> - </param> - <when value="dirichlet"> - <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" /> - <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" /> - </when> - <when value="dmix"> - <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" /> - <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" /> - </when> - <when value="mega"> - <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" /> - <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" /> - </when> - <when value="megap"> - <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" /> - <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" /> - </when> - <when value="addone"> - <!-- no values here? --> - </when> - </conditional> - <conditional name="spmap_type"> - <param name="spmap_type_selector" type="select" label="EM starting points"> - <option value="uni">uni</option> - <option value="pam" selected="true">pam</option> - <option value="cons">Use starting point from string</option> - </param> - <when value="uni"> - <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" /> - </when> - <when value="pam"> - <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" /> - </when> - <when value="cons"> - <param name="cons" type="text" value="" label="Starting point from string" /> - </when> - </conditional> - </when> - <when value="dna"> - <param name="revcomp" label="Check reverse complement" type="boolean" truevalue="-revcomp" falsevalue="" checked="False"/> - <param name="pal" label="Check for palindromes" type="boolean" truevalue="-pal" falsevalue="" checked="False"/> - <conditional name="prior_type"> - <param name="prior_type_selector" type="select" label="Sequence Alphabet"> - <option value="dirichlet" selected="true">simple Dirichlet prior</option> - <option value="dmix">mixture of Dirichlets prior</option> - <option value="mega">extremely low variance dmix</option> - <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option> - <option value="addone">add +1 to each observed count</option> - </param> - <when value="dirichlet"> - <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" /> - <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" /> - </when> - <when value="dmix"> - <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" /> - <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" /> - </when> - <when value="mega"> - <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" /> - <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" /> - </when> - <when value="megap"> - <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" /> - <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" /> - </when> - <when value="addone"> - <!-- no values here? --> - </when> - </conditional> - <conditional name="spmap_type"> - <param name="spmap_type_selector" type="select" label="EM starting points"> - <option value="uni" selected="true">uni</option> - <option value="pam">pam</option> - <option value="cons">Use starting point from string</option> - </param> - <when value="uni"> - <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" /> - </when> - <when value="pam"> - <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" /> - </when> - <when value="cons"> - <param name="cons" type="text" value="" label="Starting point from string" /> - </when> - </conditional> - </when> - </conditional> - - <param name="nmotifs" type="integer" value="1" label="Number of different motifs to search" /> - <param name="maxsize" type="integer" value="1000000" label="Max number of characters in the sequence file"/> - <param name="evt" type="float" value="inf" label="E-value to stop looking for motifs" /> - <conditional name="mod_type"> - <param name="mod_type_selector" type="select" label="Expected motif distribution"> - <option value="oops">One Occurrence Per Sequence</option> - <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option> - <option value="anr">Any Number of Repetitions</option> - </param> - <when value="oops"> - <!-- no values here --> - </when> - <when value="zoops"> - <conditional name="motif_occurrence_type"> - <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences"> - <option value="default" selected="true">Use defaults</option> - <option value="nsites">nsites</option> - <option value="min_max_sites">min and max sites</option> - </param> - <when value="default"> - <!-- no values here --> - </when> - <when value="nsites"> - <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" /> - </when> - <when value="min_max_sites"> - <param name="minsites" type="integer" value="1" label="minsites" /> - <param name="maxsites" type="integer" value="50" label="maxsites" /> - </when> - </conditional> - </when> - <when value="anr"> - <conditional name="motif_occurrence_type"> - <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences"> - <option value="default" selected="true">Use defaults</option> - <option value="nsites">nsites</option> - <option value="min_max_sites">min and max sites</option> - </param> - <when value="default"> - <!-- no values here --> - </when> - <when value="nsites"> - <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" /> - </when> - <when value="min_max_sites"> - <param name="minsites" type="integer" value="1" label="minsites" /> - <param name="maxsites" type="integer" value="50" label="maxsites" /> - </when> - </conditional> - </when> - </conditional> - <param name="wnsites" type="float" value="0.8" label="Weight on the prior on nsites" /> - - <conditional name="motif_width_type"> - <param name="motif_width_type_selector" type="select" label="Motif width type"> - <option value="exact">Exact width</option> - <option value="range" selected="true">Specify a range</option> - </param> - <when value="exact"> - <param name="width" type="integer" value="10" label="Width of motif to search" /> - </when> - <when value="range"> - <param name="minw" type="integer" value="8" label="Min width of motif to search" /> - <param name="maxw" type="integer" value="50" label="Max width of motif to search" /> - </when> - </conditional> - - <conditional name="motif_trim_type"> - <param name="motif_trim_type_selector" type="select" label="Motif trim type"> - <option value="nomatrim">No motif trim</option> - <option value="trim" selected="true">Trim motif</option> - </param> - <when value="nomatrim"> - <!-- no values here --> - </when> - <when value="trim"> - <param name="wg" type="integer" value="11" label="Gap cost" /> - <param name="ws" type="integer" value="1" label="Space cost" /> - <param name="noendgaps" label="Do not penalize endgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False"/> - </when> - </conditional> - - <param name="bfile" type="data" format="txt" optional="True" label="Background Model" /> - <param name="pspfile" type="data" format="txt" optional="True" label="Position-Specific Prior" /> - - <param name="maxiter" type="integer" value="50" label="Number of iterations of EM to run" /> - <param name="distance" type="float" value="0.001" label="Convergence criterion" /> - - <conditional name="branching_type"> - <param name="branching_type_selector" type="select" label="x-branching type"> - <option value="x_branch">Perform x-branching</option> - <option value="no_x_branch" selected="true">No x-branching</option> - </param> - <when value="no_x_branch"> - <!-- no values here --> - </when> - <when value="x_branch"> - <param name="bfactor" type="integer" value="3" label="Number of iterations of branching" /> - <param name="heapsize" type="integer" value="64" label="Maximum number of heaps to use" /> - </when> - </conditional> - - </when> - </conditional> - - <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"> - <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> - </param> - - </inputs> - <outputs> - <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/> - <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)"/> - <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"/> - </outputs> - <tests> - <test> - <param name="input1" value="meme/meme/meme_input_1.fasta" ftype="fasta" dbkey="hg19"/> - <param name="options_type_selector" value="basic"/> - <param name="non_commercial_use" value="True"/> - <output name="html_outfile" file="meme/meme/meme_output_html_1.html" lines_diff="12"/> - <output name="txt_outfile" file="meme/meme/meme_output_txt_1.txt" lines_diff="12"/> - <output name="xml_outfile" file="meme/meme/meme_output_xml_1.xml" lines_diff="8"/> - </test> - </tests> - <help> - -.. class:: warningmark - -**WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. Before using, be sure to review, agree, and comply with the license.** - -If you want to specify sequence weights, you must include them at the top of your input FASTA file. - -.. class:: infomark - -**To cite MEME:** -Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. - - -For detailed information on MEME, click here_. To view the license_. - -.. _here: http://meme.nbcr.net/meme/meme-intro.html -.. _license: http://meme.nbcr.net/meme/COPYRIGHT.html - - </help> -</tool>