Mercurial > repos > iuc > meme_meme
diff meme.xml @ 9:794b2859c286 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
| author | iuc |
|---|---|
| date | Thu, 29 Jun 2017 20:39:45 -0400 |
| parents | 487ce3fa1822 |
| children | b8c05adb68da |
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--- a/meme.xml Mon Nov 14 13:17:41 2016 -0500 +++ b/meme.xml Thu Jun 29 20:39:45 2017 -0400 @@ -1,87 +1,78 @@ -<tool id="meme_meme" name="MEME" version="4.11.1.0"> +<tool id="meme_meme" name="MEME" version="4.11.2.0"> <description>- Multiple Em for Motif Elicitation</description> - <requirements> - <requirement type="package" version="1.3.20">graphicsmagick</requirement> - <requirement type="package" version="4.11.1">meme</requirement> - </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> - <command> - <![CDATA[ - meme "$input1" - -o "${html_outfile.files_path}" - -nostatus - -maxsize 1000000 - #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}" - #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 - #end if - && 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 ${xml_outfile} - ]]> - </command> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +meme '$input1' +-o '${html_outfile.files_path}' +-nostatus +-maxsize 1000000 +#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}' + #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 '${options_type.branching_type.heapsize}' + #end if +#end if +&& mv '${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">