changeset 49:94b3643ce679 draft

Uploaded

--- a/peakMotifs_wrapper.xml	Thu Sep 24 09:44:54 2015 -0400
+++ b/peakMotifs_wrapper.xml	Tue Sep 29 07:37:17 2015 -0400
@@ -13,11 +13,8 @@
 
 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_peak_motifs" name="RSAT Peak Motifs" version="1.0">
+<tool id="rsat_peak_motifs" name="RSAT Peak Motifs" version="2.0">
   <description>Create Logo images from peaks</description>
-  <requirements>
-    <requirement type="package" version="0.6">python_suds</requirement>
-  </requirements>
   <command interpreter="python">
     peakMotifs_wrapper.py -test $fastaFile -outGalaxy $htmlFile
     #if $control_conditional.controle_file == "yes":
@@ -219,24 +216,19 @@
 
 *Partial results :*
 
-.. image:: $PATH_TO_IMAGES/result_peak_motifs_1.png
+.. image:: ${static_path}/images/result_peak_motifs_1.png
   :height: 350
   :width: 600
 
-.. image:: $PATH_TO_IMAGES/result_peak_motifs_2.png
+.. image:: ${static_path}/images/result_peak_motifs_2.png
   :height: 250
   :width: 600
 
+------
+
+**Citation**
+
+For the underlying tool, please cite `Thomas-Chollier, M., Herrmann, C., Defrance, M., Sand, O., Thieffry, D. and van Helden, J. (2011). RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Research doi:10.1093/nar/gkr1104, 9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/22156162&gt;`_
+
   </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>