Mercurial > repos > proteore > proteore_prot_features

diff prot_features.xml @ 1:bfc679370c64 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
author proteore
date Fri, 16 Feb 2018 04:06:16 -0500
parents e3b52db3d583
children 6659a32876ea
line wrap: on
line diff
--- a/prot_features.xml	Sun Nov 26 19:45:52 2017 -0500
+++ b/prot_features.xml	Fri Feb 16 04:06:16 2018 -0500
@@ -1,6 +1,6 @@
 <tool id="prot_features" name="Protein Features (neXtProt)" version="0.1.0">
 <description>
-obtains different features of your protein list from neXtProt.
+Annotate your protein list using features retrieved from neXtProt database.
 </description>
 <requirements>
 </requirements>
@@ -9,54 +9,55 @@
 </stdio>
 <command><![CDATA[
 
-  #if $inputtype.filetype == "copy_paste":  
-    Rscript --vanilla $__tool_directory__/get_data_nextprot.R --inputtype copypaste --input '$inputtype.genelist' --nextprot $__tool_directory__/result_nextprot.txt --column c1 --argsP1 '$Nextprot_params.P1' --argsP2 '$Nextprot_params.P2'--argsP3 '$Nextprot_params.P3' --type '$idtype' --output '$output' --header None 
+  #if $inputtype.filetype == "copy_paste":
+    
+      Rscript $__tool_directory__/protein_features.R --inputtype=copypaste --input='$inputtype.genelist' --nextprot=$__tool_directory__/result_nextprot.txt --column=c1 --argsP1='$Nextprot_params.P1' --argsP2='$Nextprot_params.P2' --argsP3='$Nextprot_params.P3' --type='$idtype' --output='$output' --header=None 
+    
   #end if
 
   #if $inputtype.filetype == "file_all": 
   
-  Rscript --vanilla $__tool_directory__/get_data_nextprot.R --inputtype tabfile --input '$inputtype.genelist' --nextprot $__tool_directory__/result_nextprot.txt --column '$inputtype.column' --argsP1 '$Nextprot_params.P1' --argsP2 '$Nextprot_params.P2'--argsP3 '$Nextprot_params.P3' --type '$idtype' --output '$output' --header '$inputtype.header' 
+      Rscript $__tool_directory__/protein_features.R --inputtype=tabfile --input='$inputtype.genelist' --nextprot=$__tool_directory__/result_nextprot.txt --column='$inputtype.column' --argsP1='$Nextprot_params.P1' --argsP2='$Nextprot_params.P2' --argsP3='$Nextprot_params.P3' --type='$idtype' --output='$output' --header='$inputtype.header' 
 
   #end if
     
-
 ]]></command>
 
 <inputs>
   <conditional name="inputtype">
     <param name="filetype" type="select" label="Select your type of input file"> 
-      <option value="file_all">Input file containing your identifiers</option>
+      <option value="file_all">Input file containing your identifiers (neXtProt or Uniprot ID)</option>
       <option value="copy_paste">Copy/paste your list of IDs</option> 
     </param>
     <when value="copy_paste">
       <param name="genelist" type="text" label="Enter a list of identifiers"/>
     </when>
     <when value="file_all">
-      <param name="genelist" type="data" format="txt,tabular" label="Choose a multiple-columns file" help="This file must imperatively have 1 column filled with IDs consistent with the database that will be used. Please use the MappingIDs component if this is not the case."/>
-      <param name="column" type="text" label="Please specify the column where you would like to apply the comparison (e.g : Enter c1)" value="c1"/> 
+      <param name="genelist" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="This file must imperatively have 1 column filled with IDs consistent with the neXtprot database (Uniprot accession number or neXtProt ID). If this is not the case, please use the ID_Converter tool."/>
+      <param name="column" type="text" label="Please specify the column where are your IDs (e.g : Enter c1 for column n°1)" value="c1"/> 
       <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false"> 
- 	  <option value="TRUE" selected="true">Yes</option>
-          <option value="FALSE" selected="false">No</option>
+ 		      <option value="true" selected="true">Yes</option>
+          <option value="false" selected="false">No</option>
       </param>
     </when>
   </conditional>
+
       <param name="idtype" type="select" label="Type of your input ids" multiple="false" optional="false"> 
- 	  <option value="nextprot" selected="false">Nextprot IDs</option>
-          <option value="uniprot" selected="true">Uniprot IDs</option>
+ 		      <option value="uniprot" selected="true">Uniprot accession number</option>
+          <option value="nextprot" selected="false">neXtProt IDs</option>
       </param>
-
-      <section name="Nextprot_params" title="Choose the type of information (compulsory step)" expanded="True">
+      <section name="Nextprot_params" title="Select features of interest (compulsory step)" expanded="True">
         <param name="P1" type="select" label="Physico-Chemical Features" multiple="true" help="Choose the information you want to add to your data from Nextprot" display="checkboxes" optional="true"> 
+          <option value="SeqLength" selected="false">Sequence Length</option>
           <option value="MW" selected="false">Molecular Weight</option>
- 	  <option value="SeqLength" selected="false">Sequence Length</option>
           <option value="IsoPoint" selected="false">Isoelectric point</option>
           <option value="TMDomains" selected="false">Number of transmembrane domains</option>
-          <option value="ProteinExistence" selected="false">Protein Existence (PE level)</option>
+          <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option>
         </param>
 
         <param name="P2" type="select" label="Localization" multiple="true" help="Choose the information you want to add to your data from Nextprot" display="checkboxes" optional="true"> 
- 	  <option value="Chr" selected="false">Chromosome</option>
- 	  <option value="SubcellLocations" selected="false">Subcellular Location</option>
+ 		      <option value="Chr" selected="false">Chromosome</option>
+ 		      <option value="SubcellLocations" selected="false">Subcellular Location</option>
         </param>
 
         <param name="P3" type="select" label="Diseases information">
@@ -69,77 +70,58 @@
 
 
 <outputs>
-  <data name="output" format="tsv" label="Add information from ${database_type.database}"/>
-
-
+  <data name="output" format="tsv" label="Add information from neXtProt"/>
 </outputs>
 
-
 <tests>
   <test>
     <conditional name="inputtype">
       <param name="filetype " value="tabfile"/>
-      <param name="genelist" value="mitochondrion_enzymes_Nextprot.txt"/>
+      <param name="genelist" value="FKW_ID_Converter_Lacombe_et_al_2017_OK.txt"/>
       <param name="column" value="c1"/>
-      <param name="header" value="TRUE"/>
+      <param name="header" value="true"/>
     </conditional>
 
-    <param name="idtype" value="nextprot"/> 
+    <param name="idtype" value="uniprot"/> 
 
-      <section name="Nextprot_params">
-        <param name="P1" value="MW,SeqLength,IsoPoint,TMDomains,ProteinExistence"/> 
-        <param name="P2" value="Chr,SubcellLocations"/> 
-        <param name="P3" value="Diseases"/> 
-      </section>
-
-    <output name="output" file="output_get_data.tsv"/>
+    <section name="Nextprot_params">
+      <param name="P1" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/> 
+      <param name="P2" value="Chr,SubcellLocations"/> 
+      <param name="P3" value="Diseases"/> 
+    </section>
+      
+    <output name="output" file="Add_information_from_neXtProt.tsv"/>
   </test>
 </tests>
 
 <help><![CDATA[
 
-This tool filters an input **tabular** file according to different databases.
+This tool add annotation (protein features) from neXtProt database (knowledge base on human proteins) to your protein IDs list.
 
 **Input**
 
-Input can be a file containing multiple fields but with **at least one column of Ensembl gene IDs** or a list of Ensembl gene ids. If your input file contains other kind of IDs, please refer to the MappingIDs component to create a column of Ensembl gene IDs.  
+Input can be a file containing multiple fields but with **at least one column of Uniprot accession number or neXtProt IDs**. If your input file contains other type of IDs, please use the ID_Converter tool.  
 
 **Databases**
 
-The input file will be filtered using information from different sources : 
-
-- HPA normal tissue : will filter the input according to the data contained in the Human Protein Atlas webservice. Pertinent information, such as tissular location, will be added for each gene to your input file.  
-
-- HPA cancer tissue :  will filter the input according to the data contained in the Human Protein Atlas webservice for cancer. Pertinent information, such as tumor type, will be added for each gene to your input file.  
-
-**Parameters**
-
-For HPA normal tissue :
-
-- tissue category : categories based on RNA-Seq data to estimate the transcript abundance of each protein-coding gene in tissues. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#rna .
-
-- level of detection IF : level of detection of the protein associated to the coding gene tissues based on immunofluorescency. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if .
-
-- level of detection IH :  level of detection of the protein associated to the coding gene tissues based on immunohistochemistry. For more information, please refer to http://www.proteinatlas.org/about/assays+annotation#if .
-
-For HPA cancer tissue : 
-
-- tumors : which tumors are associated with your protein-coding genes according to the Human Protein Atlas.
-
+Annotations have been retrieved from the neXtProt database (Gaudet et  al., 2017) via a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985)
 
 **Outputs**
 
-The output will be a tabular file. The initial columns will be kept, but lines can be deleted due to the filtering process. Additional columns will be added according to which data you chose to filter your input with.  
+The output is a tabular file. The initial columns are kept and columns are be added according to which annotation you have selected.  
+
+**Authors**
 
+T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
 
-**Data sources**
+Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
 
-The data for HPA normal tissue was retrieved from the Human Protein Atlas downloadable data repository (http://www.proteinatlas.org/download/proteinatlas.tab.gz).
+This work has been partially funded through the French National Agency for Research (ANR) IFB project.
 
-The data for HPA cancer was retrieved from the Human Protein Atlas downloadable data repository (http://www.proteinatlas.org/download/cancer.csv.zip).
-]]></help>
-
-<citations>
-</citations>
+Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
+ 
+    ]]></help>
+    <citations>
+    </citations>
 
 </tool>