changeset 0:306027d1b16e draft default tip

Uploaded

--- /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>