Mercurial > repos > qfab > meme_ws
changeset 0:306027d1b16e draft default tip
Uploaded
author | qfab |
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date | Tue, 02 Sep 2014 19:28:57 -0400 |
parents | |
children | |
files | meme_ws/README.txt meme_ws/meme.xml meme_ws/tool_dependencies.xml |
diffstat | 3 files changed, 222 insertions(+), 0 deletions(-) [+] |
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--- /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. +
--- /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 @@ +<tool id="meme" name="MEME" version="1.0.0"> + <requirements> + <requirement type='package' version="2.4.1">opal</requirement> + <requirement type='package' version="1.0.0">meme_ws</requirement> + </requirements> + <description>- Multiple Em for Motif Elicitation</description> + <command>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 + + </command> + <inputs> + <param format="fasta" name="input1" type="data" label="Sequences"/> + + <param name="mirror" label="Which Mirror would you like to use" type="select"> + <option value="ebi" selected="true">BRAEMBL(Australia)</option> + <option value="nbcr">NBCR(US)</option> + </param> + + + <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"> + <!-- do nothing here --> + </when> + <when value="advanced"> + + + <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="dna"> + <param name="revcomp" label="Check reverse complement" type="boolean" truevalue="" falsevalue="-norevcomp" checked="True"/> + <param name="pal" label="Check for palindromes" type="boolean" truevalue="-pal" falsevalue="" checked="False"/> + </when> + </conditional> + + <param name="nmotifs" type="integer" value="3" label="Number of different motifs to search" /> + <conditional name="mod_type"> + <param name="mod_type_selector" type="select" label="Expected motif distribution"> + <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"> + <!-- no values here --> + </when> + <when value="zoops"> + + <param name="minsites" type="integer" value="6" label="minsites" /> + <param name="maxsites" type="integer" value="50" label="maxsites" /> + </when> + <when value="anr"> + <param name="minsites" type="integer" value="6" label="minsites" /> + <param name="maxsites" type="integer" value="50" label="maxsites" /> + </when> + </conditional> + + <param name="minw" type="integer" value="8" label="Min width of motif to search" /> + <param name="maxw" type="integer" value="50" label="Max width of motif to search" /> + + + <param name="bfile" type="data" format="txt" optional="True" label="Background Model" /> + <param name="neg" type="data" format="txt" optional="True" label="Negative Sequences Set(PSPs generation)" /> + + </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="txt" name="outputtxt" label="${tool.name} on ${on_string} (text)"/> + <data format="xml" name="outputxml" label="${tool.name} on ${on_string} (xml)"/> + <data format="html" name="html_file" file="index.html" label="${tool.name} on ${on_string} (html)"/> + + </outputs> + <tests> + <test> + <param name="input1" value="meme_out/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_out/meme.html" lines_diff="12"/> + <output name="txt_outfile" file="meme_out/meme.txt" lines_diff="12"/> + <output name="xml_outfile" file="meme_out/meme.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. + +.. 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 + + </help> +</tool>
--- /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 @@ +<?xml version="1.0"?> + <tool_dependency> + <package name="opal" version="2.4.1"> + <repository changeset_revision="7b3a57b17ef5" name="package_opal_2_4_1" owner="qfab" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + </package> + <package name="meme_ws" version="1.0.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://bitbucket.org/qfab/meme/downloads/MemeWs.tgz</action> + <action type="make_directory">$INSTALL_DIR/meme</action> + <action type="set_environment_for_install"> + <repository changeset_revision="7b3a57b17ef5" name="package_opal_2_4_1" owner="qfab" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" > + <package name="opal" version="2.4.1" /> + </repository> + </action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/meme/</destination_directory> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_OPAL]</environment_variable> + <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_ZSI]</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/meme/</environment_variable> + </action> + </actions> + </install> + <readme></readme> + </package> +</tool_dependency>