annotate meme.xml @ 0:e416c7c26977 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1

<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>