# HG changeset patch
# User qfab
# Date 1409700537 14400
# Node ID 306027d1b16eeb3b85aa9491f6cd1794961f1630
Uploaded
diff -r 000000000000 -r 306027d1b16e meme_ws/README.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/meme_ws/README.txt Tue Sep 02 19:28:57 2014 -0400
@@ -0,0 +1,32 @@
+Galaxy wrappers for MEME
+=========================================================================
+MEME is a tool for discovering motifs in a group of related DNA or protein
+sequences.
+
+Requirements
+=========================================================================
+Please note, 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
+(http://meme.nbcr.net/meme/COPYRIGHT.html).
+
+Disclaimer
+=========================================================================
+This source code is provided by QFAB Bioinformatics "as is", in the hope that
+it will be
+useful, and any express or implied warranties, including, but not limited to,
+the implied warranties of merchantability and fitness for a particular purpose
+are disclaimed.
+IN NO EVENT SHALL QFAB BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES HOWEVER CAUSED AND ON ANY THEORY
+OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT(INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOURCE
+CODE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+License
+=========================================================================
+This work by QFAB Bioinformatics (as part of the GVL project
+http://genome.edu.au)
+is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0
+International License.
+
diff -r 000000000000 -r 306027d1b16e meme_ws/meme.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/meme_ws/meme.xml Tue Sep 02 19:28:57 2014 -0400
@@ -0,0 +1,161 @@
+
+
+ opal
+ meme_ws
+
+ - Multiple Em for Motif Elicitation
+ meme_ws
+
+ -mirror ${mirror}
+
+ #if str( $options_type.options_type_selector ) == 'advanced':
+ -alpha ${options_type.alphabet_type.alphabet_type_selector}
+ -mod "${options_type.mod_type.mod_type_selector}"
+ -nmotifs "${options_type.nmotifs}"
+
+
+ #if str( $options_type.mod_type.mod_type_selector ) != 'oops':
+ -minsites "${options_type.mod_type.minsites}" -maxsites "${options_type.mod_type.maxsites}"
+ #end if
+
+ -minw "${options_type.minw}" -maxw "${options_type.maxw}"
+
+
+ #if str( $options_type.bfile ) != 'None':
+ -bfile "${options_type.bfile}"
+ #end if
+
+ #if str( $options_type.neg ) != 'None':
+ -neg "${options_type.neg}"
+ #end if
+
+
+
+ #if str( $options_type.alphabet_type.alphabet_type_selector ) == "dna":
+ ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal}
+ #end if
+
+
+
+ ##-maxsize "1000000" ##remove hardcoded maxsize? should increase number of processors instead
+
+ #end if
+
+ "$input1"
+
+ $outputtxt
+ $outputxml
+ $html_file.files_path
+ $html_file
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+.. 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_.
+
+------
+
+**Citation**
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
+.. _here: http://meme.nbcr.net/meme/meme-intro.html
+.. _license: http://meme.nbcr.net/meme/COPYRIGHT.html
+
+
+
diff -r 000000000000 -r 306027d1b16e meme_ws/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/meme_ws/tool_dependencies.xml Tue Sep 02 19:28:57 2014 -0400
@@ -0,0 +1,29 @@
+
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+ https://bitbucket.org/qfab/meme/downloads/MemeWs.tgz
+ $INSTALL_DIR/meme
+
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+ .
+ $INSTALL_DIR/meme/
+
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+ $ENV[PYTHONPATH_OPAL]
+ $ENV[PYTHONPATH_ZSI]
+ $INSTALL_DIR/meme/
+
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