view convertMatrix_wrapper.xml @ 52:a1d369ead6d7 draft default tip

Uploaded

<!--Convert Matrix - developed by Jocelyn Brayet <[e-mail]>
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="0.6">python_suds</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>