Mercurial > repos > jbrayet > rsat
changeset 21:afb729007a81 draft
Uploaded
| author | jbrayet |
|---|---|
| date | Tue, 22 Sep 2015 08:00:54 -0400 |
| parents | fb38cedce83e |
| children | 5aa022e3a2ae |
| files | dyadAnalysis_wrapper.xml |
| diffstat | 1 files changed, 183 insertions(+), 0 deletions(-) [+] |
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--- /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>