Mercurial > repos > qfab > meme_ws_d

--- a/meme_ws/README.txt	Tue Sep 02 19:22:15 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-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.
-
--- a/meme_ws/meme.xml	Tue Sep 02 19:22:15 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,161 +0,0 @@
-<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>
--- a/meme_ws/tool_dependencies.xml	Tue Sep 02 19:22:15 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-<?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>