# HG changeset patch
# User jbrayet
# Date 1442923266 14400
# Node ID 5aa022e3a2aefc4ad74d8821c129d459339f246b
# Parent  afb729007a812cfe69b3eaf66334855ce75b16ca
Uploaded

diff -r afb729007a81 -r 5aa022e3a2ae convertMatrix_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convertMatrix_wrapper.xml	Tue Sep 22 08:01:06 2015 -0400
@@ -0,0 +1,178 @@
+<!--Convert Matrix - 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_convert_matrix" name="RSAT Convert Matrix" version="1.0">
+  <description>Inter-conversions between various formats of PSSM</description>
+  <requirements>
+    <requirement type="package" version="2.7">python</requirement>
+  </requirements>
+  <command interpreter="python">
+    convertMatrix_wrapper.py -matrix $matrixFile -outGalaxy $txtFile -server $server -input_form $input_format -output_form $output_format
+    #if $advanced_parameters.adv_param == "show":
+      #if $advanced_parameters.return_count_condition.return_count == "yes":
+        -return counts
+        -perm $advanced_parameters.return_count_condition.perm
+      #else:
+        -return $advanced_parameters.return_count_condition.return
+      #end if
+      -rc $advanced_parameters.rc
+      -decimals $advanced_parameters.decimals
+    #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" type="data" format="txt" label="Matrix (or matrices) (TXT file)" />
+    <param name="input_format" type="select" label="Matrix input format">
+        <option value="tab" selected="true">tab</option>
+        <option value="alignace" >alignace</option>
+        <option value="assembly" >assembly</option>
+        <option value="cb" >cb</option>
+        <option value="clustal" >clustal</option>
+        <option value="consensus" >consensus</option>
+        <option value="feature" >feature</option>
+        <option value="gibbs" >gibbs</option>
+        <option value="infogibbs" >infogibbs</option>
+        <option value="meme" >meme</option>
+        <option value="motifsampler" >motifsampler</option>
+        <option value="transfac" >transfac</option>
+        <option value="jaspar" >jaspar</option>
+    </param>
+    <param name="output_format" type="select" label="Output format">
+        <option value="transfac" selected="true">transfac</option>
+        <option value="consensus" >consensus</option>
+        <option value="tab" >tab</option>
+        <option value="jaspar" >jaspar</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="return_count_condition" >
+          <param name="return_count" type="select" label="Counts option in output field" help="" >
+            <option value="yes" selected="true">Yes</option>
+            <option value="no">No</option>
+          </param>
+          <when value="yes">
+            <param name="perm" type="integer" value="0" label="Permutations" help="" />
+          </when>
+          <when value="no">
+            <param name="return" type="select" display="checkboxes" multiple="True" label="Output fields">
+              <option value="consensus" selected="true">consensus</option>
+              <option value="parameters" selected="true">parameters</option>
+              <option value="info" >info</option>
+              <option value="frequencies" >frequencies</option>
+              <option value="logo" >logo</option>
+              <option value="margins" >margins</option>
+              <option value="profile" >profile</option>
+              <option value="sites" >sites</option>
+              <option value="wdistrib" >wdistrib</option>
+              <option value="weights" >weights</option>
+              <validator type="no_options" message="You must select at least one result type." />
+            </param>
+          </when>
+        </conditional>
+        <param name="rc" type="select" label="Compute reverse complement" help="" >
+          <option value="0" selected="true">No</option>
+          <option value="1">Yes</option>
+        </param>
+        <param name="decimals" type="select" label="Score decimals" help="" >
+          <option value="0" >0</option>
+          <option value="1" selected="true">1</option>
+          <option value="2">2</option>
+        </param>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="txt" name="txtFile" label="RSAT output - convertMatrix results" />
+  </outputs>
+  <help>
+
+**What it does**
+
+.. class:: infomark
+
+Convert different types of position-specific scoring matrices (PSSM), and calculate statistical parameters.
+
+------
+
+*Example with jaspar matrix*::
+
+ >matrix1 matrix1
+ A [ 4 19 0 0 0 0 ]
+ C [ 16 0 20 0 0 0 ]
+ G [ 0 1 0 20 0 20 ]
+ T [ 0 0 0 0 20 0 ]
+
+------
+
+*Results : tranfac matrix with output fields (consensus, parameters, frequencies and sites)*::
+
+ AC  m1
+ XX
+ ID  m1
+ XX
+ DE  m1 m1; from JASPAR
+ P0       A     C     G     T
+ 1        4    16     0     0
+ 2       19     0     1     0
+ 3        0    20     0     0
+ 4        0     0    20     0
+ 5        0     0     0    20
+ 6        0     0    20     0
+ XX
+ CC  program: jaspar
+ CC  matrix.nb: 1
+ CC  min.prior: 0.25
+ CC  alphabet.size: 4
+ CC  max.bits: 2
+ CC  total.information: 6.56407409450406
+ CC  information.per.column: 1.09401234908401
+ CC  max.possible.info.per.col: 1.38629436111989
+ CC  consensus.strict: CACGTG
+ CC  consensus.strict.rc: CACGTG
+ CC  consensus.IUPAC: CACGTG
+ CC  consensus.IUPAC.rc: CACGTG
+ CC  consensus.regexp: CACGTG
+ CC  consensus.regexp.rc: CACGTG
+ CC  residues.content.crude.freq: a:0.1917|c:0.3000|g:0.3417|t:0.1667
+ CC  G+C.content.crude.freq: 0.641666666666667
+ CC  residues.content.corrected.freq: a:0.1944|c:0.2976|g:0.3373|t:0.1706
+ CC  G+C.content.corrected.freq: 0.634920634920635
+ XX
+ //
+  </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>