# HG changeset patch
# User mvdbeek
# Date 1432826103 14400
# Node ID 838fd0e0e13c673c1a4e4476002520d61b603464
planemo upload for repository http://meme-suite.org/tools/meme
diff -r 000000000000 -r 838fd0e0e13c meme.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/meme.xml Thu May 28 11:15:03 2015 -0400
@@ -0,0 +1,351 @@
+
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+ meme
+
+ motif discovery
+ 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}
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+ && mv ${html_outfile.files_path}/meme.txt ${txt_outfile}
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+ && mv ${html_outfile.files_path}/meme.xml ${xml_outfile}
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+.. class:: warningmark
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+**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.
+
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+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
+
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+
diff -r 000000000000 -r 838fd0e0e13c tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu May 28 11:15:03 2015 -0400
@@ -0,0 +1,6 @@
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