Mercurial > repos > jbrayet > rsat

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compareMatrices_wrapper.xml	Tue Sep 22 08:01:16 2015 -0400
@@ -0,0 +1,131 @@
+<!--Compare Matrices - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
+Copyright (C) 2015  Institut Curie
+
+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 3 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.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.-->
+<tool id="rsat_compare_matrices" name="RSAT Compare Matrices" version="1.0">
+  <description>Comparison between two collections of position-specific scoring matrices</description>
+  <requirements>
+    <requirement type="package" version="2.7">python</requirement>
+  </requirements>
+  <command interpreter="python">
+    compareMatrices_wrapper.py -matrix_1 $matrixFile_1 -format1 $matrix_format_1 -matrix_2 $matrixFile_2 -format2 $matrix_format_2 -outGalaxy $txtFile -server $server
+    #if $advanced_parameters.adv_param == "show":
+      #if $advanced_parameters.allReturn.all_return == "no":
+        -returnResults $advanced_parameters.allReturn.return
+      #else:
+        -returnResults all
+      #end if
+    #end if
+  </command>
+  <inputs>
+    <param name="server" type="select" label="RSAT server (if Time out error, change server)" >
+      <option value="fr_ens" selected="true">RSAT Protists</option>
+      <option value="fr_mrs" >RSAT Fungis</option>
+      <option value="fr_ro" >RSAT Metazoa</option>
+      <option value="fr_mrs_2" >RSAT Teaching</option>
+      <option value="es" >RSAT Plants</option>
+      <option value="mx" >RSAT Prokaryotes</option>
+    </param>
+    <param name="matrixFile_1" type="data" format="txt" label="Matrix (or matrices) (TXT file)" />
+    <param name="matrix_format_1" type="select" label="Matrix 1 format" help="" >
+      <option value="tab" selected="true">tab</option>
+      <option value="cb" >cb</option>
+      <option value="transfac" >transfac</option>
+      <option value="jaspar" >jaspar</option>
+      <option value="consensus" >consensus</option>
+      <option value="gibbs" >gibbs</option>
+      <option value="meme" >meme</option>
+      <option value="assembly" >assembly</option>
+    </param>
+    <param name="matrixFile_2" type="data" format="txt" label="Matrix (or matrices) (TXT file)" />
+    <param name="matrix_format_2" type="select" label="Matrix 2 format" help="" >
+      <option value="tab" selected="true">tab</option>
+      <option value="cb" >cb</option>
+      <option value="transfac" >transfac</option>
+      <option value="jaspar" >jaspar</option>
+      <option value="consensus" >consensus</option>
+      <option value="gibbs" >gibbs</option>
+      <option value="meme" >meme</option>
+      <option value="assembly" >assembly</option>
+    </param>
+    <conditional name="advanced_parameters" >
+      <param name="adv_param" type="select" label="Advanced Parameters" help="" >
+        <option value="hide" selected="true">Hide</option>
+        <option value="show">Show</option>
+      </param>
+      <when value="hide" />
+      <when value="show">
+        <conditional name="allReturn" >
+          <param name="all_return" type="select" label="All supported output fields, including all metrics" >
+            <option value="yes" selected="true">Yes</option>
+            <option value="no">No</option>
+          </param>
+          <when value="yes" />
+          <when value="no">
+            <param name="return" type="select" display="checkboxes" multiple="True" label="Fields to return">
+              <option value="offset">offset</option>
+              <option value="cor">cor</option>
+              <option value="Ncor" selected="true">Ncor</option>
+              <option value="cov">cov</option>
+              <option value="SSD">SSD</option>
+              <option value="NSW">NSW</option>
+              <option value="SW">SW</option>
+              <option value="dEucl">dEucl</option>
+              <option value="NdEucl">NdEucl</option>
+              <option value="NsEucl">NsEucl</option>
+              <option value="dKL">dKL</option>
+              <option value="matrix_number">matrix_number</option>
+              <option value="matrix_id">matrix_id</option>
+              <option value="matrix_name">matrix_name</option>
+              <option value="matrix_ac">matrix_ac</option>
+              <option value="width">width</option>
+              <option value="strand" selected="true">strand</option>
+              <option value="pos">pos</option>
+              <option value="consensus">consensus</option>
+              <option value="offset_rank">offset_rank</option>
+              <option value="match_rank">match_rank</option>
+              <option value="offset_rank">offset_rank</option>
+              <option value="alignments_pairwise">alignments_pairwise</option>
+              <option value="alignments_1ton">alignments_1ton</option>
+              <option value="alignments">alignments</option>
+            </param>
+          </when>
+        </conditional>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="txt" name="txtFile" label="RSAT output - compareMatrices results" />
+  </outputs>
+  <help>
+
+**What it does**
+
+.. class:: infomark
+
+Compare two collections of position-specific scoring matrices (PSSM), and return various similarity statistics + matrix alignments (pairwise, one-to-n).
+
+  </help>
+  <citations>
+    <citation type="bibtex">@article{Medina-Rivera22042015,
+      author = {Medina-Rivera, Alejandra and Defrance, Matthieu and Sand, Olivier and Herrmann, Carl and Castro-Mondragon, Jaime A. and Delerce, Jeremy and Jaeger, Sébastien and Blanchet, Christophe and Vincens, Pierre and Caron, Christophe and Staines, Daniel M. and Contreras-Moreira, Bruno and Artufel, Marie and Charbonnier-Khamvongsa, Lucie and Hernandez, Céline and Thieffry, Denis and Thomas-Chollier, Morgane and van Helden, Jacques},
+      title = {RSAT 2015: Regulatory Sequence Analysis Tools},
+      year = {2015},
+      doi = {10.1093/nar/gkv362},
+      URL = {http://nar.oxfordjournals.org/content/early/2015/04/21/nar.gkv362.abstract},
+      eprint = {http://nar.oxfordjournals.org/content/early/2015/04/21/nar.gkv362.full.pdf+html},
+      journal = {Nucleic Acids Research}
+      }</citation>
+  </citations>
+</tool>