--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/meme.xml	Mon Dec 21 06:03:33 2015 -0500
@@ -0,0 +1,333 @@
+<tool id="meme_meme" name="MEME" version="4.11.0.0">
+    <description>- Multiple Em for Motif Elicitation</description>
+    <requirements>
+        <requirement type="package" version="4.11.0">meme</requirement>
+    </requirements>
+    <command>
+        <![CDATA[
+            meme "$input1"
+            -o "${html_outfile.files_path}"
+            -nostatus
+            #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
+            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" />
+            <when value="advanced">
+                <param name="sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set" argument="-sf"/>
+                <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" argument="-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" argument="-b"/>
+                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                            </when>
+                            <when value="dmix">
+                                <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
+                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                            </when>
+                            <when value="mega">
+                                <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
+                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                            </when>
+                            <when value="megap">
+                                <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
+                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                            </when>
+                            <when value="addone" />
+                        </conditional>
+                        <conditional name="spmap_type">
+                            <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap">
+                                <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" argument="-spfuzz"/>
+                            </when>
+                            <when value="pam">
+                                <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/>
+                            </when>
+                            <when value="cons">
+                                <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/>
+                            </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" argument="-prior">
+                                <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" argument="-b"/>
+                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                            </when>
+                            <when value="dmix">
+                                <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
+                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                            </when>
+                            <when value="mega">
+                                <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
+                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                            </when>
+                            <when value="megap">
+                                <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
+                                <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
+                            </when>
+                            <when value="addone" />
+                        </conditional>
+                        <conditional name="spmap_type">
+                            <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap">
+                                <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" argument="-spfuzz"/>
+                            </when>
+                            <when value="pam">
+                                <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/>
+                            </when>
+                            <when value="cons">
+                                <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/>
+                            </when>
+                        </conditional>
+                    </when>
+                </conditional>
+                <param name="nmotifs" type="integer" value="1" label="Number of different motifs to search" argument="-nmotifs" />
+                <param name="evt" type="float" value="inf" label="E-value to stop looking for motifs" argument="-evt"/>
+                <conditional name="mod_type">
+                    <param name="mod_type_selector" type="select" label="Expected motif distribution" argument="-mod">
+                        <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" />
+                    <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" />
+                            <when value="nsites">
+                                <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/>
+                            </when>
+                            <when value="min_max_sites">
+                                <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/>
+                                <param name="maxsites" type="integer" value="50" label="maxsites" argument="-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" />
+                            <when value="nsites">
+                                <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/>
+                            </when>
+                            <when value="min_max_sites">
+                                <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/>
+                                <param name="maxsites" type="integer" value="50" label="maxsites" argument="-maxsites"/>
+                            </when>
+                        </conditional>
+                    </when>
+                </conditional>
+                <param name="wnsites" type="float" value="0.8" label="Weight on the prior on nsites" argument="-wnsites"/>
+                <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" argument="-w"/>
+                    </when>
+                    <when value="range">
+                        <param name="minw" type="integer" value="8" label="Min width of motif to search" argument="-minw"/>
+                        <param name="maxw" type="integer" value="50" label="Max width of motif to search" argument="-maxw"/>
+                    </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" />
+                    <when value="trim">
+                        <param name="wg" type="integer" value="11" label="Gap cost" argument="-wg"/>
+                        <param name="ws" type="integer" value="1" label="Space cost" argument="-ws"/>
+                        <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" argument="-bfile"/>
+                <param name="pspfile" type="data" format="txt" optional="True" label="Position-Specific Prior" argument="-psp"/>
+                <param name="maxiter" type="integer" value="50" label="Number of iterations of EM to run" argument="-maxiter"/>
+                <param name="distance" type="float" value="0.001" label="Convergence criterion" argument="-distance"/>
+                <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" />
+                    <when value="x_branch">
+                        <param name="bfactor" type="integer" value="3" label="Number of iterations of branching" argument="-bfactor"/>
+                        <param name="heapsize" type="integer" value="64" label="Maximum number of heaps to use" argument="-heapsize"/>
+                    </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_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_output_html_1.html" compare="contains"/>
+            <output name="txt_outfile" file="meme_output_txt_1.txt" lines_diff="12"/>
+            <output name="xml_outfile" file="meme_output_xml_1.xml" lines_diff="8"/>
+        </test>
+        <test>
+            <param name="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
+            <param name="options_type_selector" value="advanced"/>
+            <param name="plib" value="prior30.plib" ftype="txt"/>
+            <param name="non_commercial_use" value="True"/>
+            <output name="html_outfile" file="meme_output_html_2.html" compare="contains"/>
+            <output name="txt_outfile" file="meme_output_txt_2.txt" lines_diff="12"/>
+            <output name="xml_outfile" file="meme_output_xml_2.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.
+
+MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences).
+MEME splits variable-length patterns into two or more separate motifs.  A motif is a sequence pattern that occurs repeatedly
+in a group of related sequences.  MEME represents motifs as position-dependent letter-probability matrices which describe the
+probability of each possible letter at each position in the pattern.  Individual MEME motifs do not contain gaps.  Patterns
+with variable-length gaps are split by MEME into two or more separate motifs.  MEME takes as input a group of sequences and
+outputs as many motifs as requested.  MEME uses statistical modeling techniques to automatically choose the best width, number
+of occurrences, and description for each motif.
+
+.. class:: infomark
+
+For detailed information on MEME, click here_, or view the license_.
+
+.. _here: http://meme-suite.org/doc/meme.html?man_type=web
+.. _license: http://meme-suite.org/doc/copyright.html?man_type=web
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @published{Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California,
+            author = {Bailey,Timothy L. and Elkan, Charles},
+            title = {Fitting a mixture model by expectation maximization to discover motifs in biopolymers},
+            year = {1994},
+            eprint = {None},
+            url = {http://www.sdsc.edu/~tbailey/papers/ismb94.pdf}
+        }</citation>
+    </citations>
+</tool>