tool_conf.xml

<?xml version='1.0' encoding='utf-8'?>
<!--
 Copyright (C) 2007-2018 Murphy Lab
 Lane Center for Computational Biology
 School of Computer Science
 Carnegie Mellon University

 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published
 by the Free Software Foundation; either version 2 of the License,
 or (at your option) any later version.

 This program is distributed in the hope that it will be useful, but
 WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 General Public License for more details.

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 along with this program; if not, write to the Free Software
 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
 02110-1301, USA.

 For additional information visit http://murphylab.web.cmu.edu or
 send email to murphy@cmu.edu
-->
<toolbox>
  <destination id="local" runner="local" >
  	<env id="CELLORGANIZER">/pylon1/mc4s8dp/icaoberg/galaxy/cellorganizer</env>
  	<env id="MATLAB">/opt/packages/matlab/R2016a/bin/matlab</env>
  	<env id="BFTOOLS">/pylon1/mc4s8dp/icaoberg/tools/bioformats/bftools</env>
  	<env id="FFMPEG">/usr/local/bin/FFMPEG</env>
  	<env id="PANDOC">/usr/local/bin/pandoc</env>
  </destination>
    
    <section id="get_data" name="Get Data">
      <tool file="data_source/upload.xml" />
      <tool file="cellorganizer/import_image.xml" />
      <tool file="cellorganizer/import_model.xml" />
      <tool file="cellorganizer/download_models_from_repository.xml" /> 
    </section>

    <!-- Model training tool -->  
    <section id="training" name="Training">
      <tool file="cellorganizer/img2slml.xml" />
    </section>

    <!-- Synthesis tool -->
    <section id="synthesis" name="Synthesis">
      <tool file="cellorganizer/slml2img.xml" />
    </section>

    <!-- These are useful tools for images-->
    <section id="cellorganizer-tools-images" name="Useful tools for images">
      <tool file="cellorganizer/export_to_vcell.xml" />
      <tool file="cellorganizer/show_3D_surface_plot.xml" />
      <tool file="cellorganizer/show_RGB_projection.xml" />
      <tool file="cellorganizer/show_projection.xml" />
      <tool file="cellorganizer/show_image_information.xml" />
    </section>


    <!-- These are useful tools for models -->
    <section id="cellorganizer-tools-models" name="Useful tools for models">
      <tool file="cellorganizer/model2info.xml" />
      <tool file="cellorganizer/slml2slml.xml" />
      <tool file="cellorganizer/show_shape_space.xml" />
    </section>

    <!-- Validators -->
    <section id="validators" name="File Validators" >
      <tool file="cellorganizer/validate_ometiff_file.xml" />
      <tool file="cellorganizer/validate_sbml_instance.xml" /> 
      <tool file="cellorganizer/validate_wavefront_obj_file.xml" /> 
      <tool file="cellorganizer/validate_dataset_list_of_ometiffs.xml" />
    </section>
</toolbox>