# HG changeset patch
# User jbrayet
# Date 1442923254 14400
# Node ID afb729007a812cfe69b3eaf66334855ce75b16ca
# Parent  fb38cedce83e55592dc90f7f7aea29774264f4a3
Uploaded

diff -r fb38cedce83e -r afb729007a81 dyadAnalysis_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dyadAnalysis_wrapper.xml	Tue Sep 22 08:00:54 2015 -0400
@@ -0,0 +1,183 @@
+<!--Dyad analysis - 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_dyad_analysis" name="RSAT Dyad Analysis" version="1.0">
+  <description>Analysis of oligomer occurrences in nucleotidic of peptidic sequences</description>
+  <requirements>
+    <requirement type="package" version="2.7">python</requirement>
+  </requirements>
+  <command interpreter="python">
+    dyadAnalysis_wrapper.py -sequence_file $sequenceFile -outGalaxy $txtFile -length $length -stats $stats -spacing $spacing -type $type
+    #if $serverChoice.server == 'fr_ens':
+        -organism $serverChoice.organism
+        -server fr_ens
+    #end if
+    #if $serverChoice.server == 'fr_mrs':
+        -organism $serverChoice.organism
+        -server fr_mrs
+    #end if
+    #if $serverChoice.server == 'fr_mrs_2':
+        -organism $serverChoice.organism
+        -server fr_mrs_2
+    #end if
+    #if $serverChoice.server == 'fr_ro':
+        -organism $serverChoice.organism
+        -server fr_ro
+    #end if
+    #if $serverChoice.server == 'mx':
+        -organism $serverChoice.organism
+        -server mx
+    #end if
+    #if $serverChoice.server == 'es':
+        -organism $serverChoice.organism
+        -server es
+    #end if
+  </command>
+  <inputs>
+    <param name="sequenceFile" type="data" format="fasta" label="Sequences File (FASTA file)" />
+    <param name="length" type="select" label="Dyad lengths" help="" >
+      <option value="3" >3</option>
+      <option value="4" selected="true">4</option>
+      <option value="5" >5</option>
+      <option value="6" >6</option>
+    </param>
+    <param name="spacing" type="select" label="Spacing between elements">
+      <option value="0" >0</option>
+      <option value="1" >1</option>
+      <option value="2" >2</option>
+      <option value="3" >3</option>
+      <option value="4" >4</option>
+      <option value="5" >5</option>
+      <option value="6" >6</option>
+      <option value="7" >7</option>
+      <option value="8" >8</option>
+      <option value="9" >9</option>
+      <option value="10" >10</option>
+      <option value="11" >11</option>
+      <option value="12" >12</option>
+      <option value="13" selected="true">13</option>
+      <option value="14" >14</option>
+      <option value="15" >15</option>
+      <option value="16" >16</option>
+      <option value="17" >17</option>
+      <option value="18" >18</option>
+      <option value="19" >19</option>
+      <option value="20" >20</option>
+      <option value="21" >21</option>
+      <option value="22" >22</option>
+    </param>
+    <conditional name="serverChoice">
+        <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>
+        <when value="fr_ens">
+            <param name="organism" type="select" label="Select an organism" help="If your organism of interest is not listed, contact the RSAT team">
+                <options from_file="RSAT_organisms_fr_ens.loc">
+                    <column name="name" index="0" />
+                    <column name="value" index="0" />
+                </options>
+            </param>
+        </when>
+        <when value="fr_mrs">
+            <param name="organism" type="select" label="Select an organism" help="If your organism of interest is not listed, contact the RSAT team">
+                <options from_file="RSAT_organisms_fr_mrs.loc">
+                    <column name="name" index="0" />
+                    <column name="value" index="0" />
+                </options>
+            </param>
+        </when>
+        <when value="fr_mrs_2">
+            <param name="organism" type="select" label="Select an organism" help="If your organism of interest is not listed, contact the RSAT team">
+                <options from_file="RSAT_organisms_fr_mrs_2.loc">
+                    <column name="name" index="0" />
+                    <column name="value" index="0" />
+                </options>
+            </param>
+        </when>
+        <when value="fr_ro">
+            <param name="organism" type="select" label="Select an organism" help="If your organism of interest is not listed, contact the RSAT team">
+                <options from_file="RSAT_organisms_fr_ro.loc">
+                    <column name="name" index="0" />
+                    <column name="value" index="0" />
+                </options>
+            </param>
+        </when>
+        <when value="mx">
+            <param name="organism" type="select" label="Select an organism" help="If your organism of interest is not listed, contact the RSAT team">
+                <options from_file="RSAT_organisms_mx.loc">
+                    <column name="name" index="0" />
+                    <column name="value" index="0" />
+                </options>
+            </param>
+        </when>
+        <when value="es">
+            <param name="organism" type="select" label="Select an organism" help="If your organism of interest is not listed, contact the RSAT team">
+                <options from_file="RSAT_organisms_es.loc">
+                    <column name="name" index="0" />
+                    <column name="value" index="0" />
+                </options>
+            </param>
+        </when>
+    </conditional>
+    <param name="stats" type="select" display="checkboxes" multiple="True" label="List of statistics to return">
+        <option value="occ" selected="true" >occ</option>
+        <option value="mseq">mseq</option>
+        <option value="freq" >freq</option>
+        <option value="proba" >proba</option>
+        <option value="ratio" >ratio</option>
+        <option value="zscore" >zscore</option>
+        <option value="like" >like</option>
+        <option value="pos" >pos</option>
+        <option value="rank" >rank</option>
+        <validator type="no_options" message="You must select at least one result type." />
+    </param>
+    <param name="type" type="select" label="Dyad type">
+      <option value="dr" >direct repeats</option>
+      <option value="ir" >inverted repeats</option>
+      <option value="rep" >any repeats</option>
+      <option value="any" selected="true" >any dyad</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="txtFile" label="RSAT output - dyadAnalysis results" />
+  </outputs>
+
+  <help>
+
+**What it does**
+
+.. class:: infomark
+
+Analysis of the statistical significance of all the spaced dyads of a given size in a sequence. Commonly used to detect over-represented spaced dyads in a set of promoter sequences.
+
+  </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>