Mercurial > repos > proteore > proteore_prot_features

diff add_protein_features.xml @ 16:7caa90759aba draft

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planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
author proteore
date Fri, 28 Jun 2019 05:05:25 -0400
parents da885fff7cf6
children 2952bae8a1ea
line wrap: on
line diff
--- a/add_protein_features.xml	Mon May 06 06:08:26 2019 -0400
+++ b/add_protein_features.xml	Fri Jun 28 05:05:25 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="prot_features" name="Add protein features" version="2019.05.06">
+<tool id="prot_features" name="Add protein features" version="2019.06.27.2">
 <description>[neXtProt]
 </description>
 <requirements>
@@ -34,7 +34,7 @@
 
 <inputs>
   <conditional name="inputtype">
-    <param name="filetype" type="select" label="Enter your IDs (neXtProt or UniProt)" help="Copy/paste or from a file" > 
+    <param name="filetype" type="select" label="Enter your IDs (neXtProt or UniProt; e.g. P05090 or NX_P05090)" help="Copy/paste or from a file" > 
       <option value="file" selected="true">Input file containing your IDs </option>
       <option value="copy_paste">Copy/paste your list of IDs</option> 
     </param>
@@ -64,28 +64,30 @@
   </conditional>
 
       <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false"> 
- 		      <option value="Uniprot_AC" selected="true">Uniprot accession number</option>
-          <option value="NextprotID" selected="false">neXtProt IDs</option>
+            <option value="NextprotID" selected="true">neXtProt IDs</option>
+ 	        <option value="Uniprot_AC" selected="false">UniProt accession number</option>
       </param>
-      <section name="Nextprot_params" title="Select features" expanded="True">
-        <param name="pc_features" type="select" label="Physico-Chemical Features" multiple="true" help="" display="checkboxes" optional="false"> 
+      <section name="Nextprot_params" title="Select features (Physico-chemical, localization, disease infiormation)" expanded="True">
+        <param name="pc_features" type="select" label="Select information to add to your list" multiple="true" help="" display="checkboxes" optional="false"> 
           <option value="SeqLength" selected="false">Sequence Length</option>
           <option value="MW" selected="false">Molecular Weight</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 (evidence score from 1 to 5)</option>
+          </param>
+
+        <param name="localization" type="select" label="Localization" multiple="true" help="" display="checkboxes" optional="true">
+          <option value="Chr" selected="false">Chromosome</option>
+ 	      <option value="SubcellLocations" selected="false">Subcellular Location</option>
         </param>
 
-        <param name="localization" type="select" label="Localization" multiple="true" help="" display="checkboxes" optional="true"> 
- 		      <option value="Chr" selected="false">Chromosome</option>
- 		      <option value="SubcellLocations" selected="false">Subcellular Location</option>
-        </param>
-
-        <param name="diseases_info" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Disease information" />
+        <param name="diseases_info" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Disease information" />
 
       </section>
       <param name="ref_file" type="select" label="Release of neXtProt reference file to use">
-        <options from_data_table="proteore_nextprot_ref"/>
+        <options from_data_table="proteore_nextprot_ref">
+            <filter type="sort_by" column="0"/>
+        </options>
       </param>
 
 </inputs>
@@ -101,13 +103,13 @@
 <tests>
   <test>
     <conditional name="inputtype">
-      <param name="filetype " value="file"/>
-      <param name="genelist" value="FKW_ID_Converter_Lacombe_et_al_2017_OK.tsv"/>
+      <param name="filetype" value="file"/>
+      <param name="genelist" value="Lacombe_et_al_2017.tsv"/>
       <param name="column" value="c1"/>
       <param name="header" value="true"/>
     </conditional>
 
-    <param name="idtype" value="uniprot"/> 
+    <param name="idtype" value="Uniprot_AC"/> 
 
     <section name="Nextprot_params">
       <param name="pc_features" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/> 
@@ -115,6 +117,7 @@
       <param name="diseases_info" value="true"/> 
     </section>
       
+    <param name="ref_file" value="test-data/cached_locally/nextprot_ref_07-05-2019.tsv"/>
     <output name="output" file="Add_information_from_neXtProt.tsv"/>
   </test>
 </tests>
@@ -131,11 +134,15 @@
 
 A list of of Uniprot Accession Number (e.g. P05090) or neXtProt IDs (e.g. NX_P05090) entered in a copy/paste mode or a file containing one or multiple columns 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.  
 
+.. class:: warningmark
+	
+In copy/paste mode, the number of IDs considered in input is limited to 5000.
+
 -----
 
 **Parameters**
 
-"Select features": three categories of annotation can be retrieved: physico-chemical features, localisation (chromosome, subcellular) and disease information (set to "Yes" by default). Select each feature according to your interest by clicking the corresponding checkbox. 
+"Select features": select each feature of your interest by clicking the corresponding checkbox. Disease information is set to "Yes" by default.  
 
 -----
 
@@ -147,10 +154,13 @@
 
 **Data source (release date)**
 
-Annotations have been retrieved from the neXtProt released on 21/02/2018 using the latest data from peptideAtlas (release January 2018)
+Annotations have been retrieved using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et  al., 2017)
 
-using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et  al., 2017)
-
+ neXtProt releases : 
+ 
+- nextProt release 07-05-2019 (release Feb 13, 2019)
+- neXtProt release 08-10-2018 (release Feb 21, 2018)
+  
 -----
 
 .. class:: infomark
@@ -163,7 +173,7 @@
 
 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
 
-Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
+Help: contact@proteore.org for any questions or concerns about this tool.
  
     ]]></help>
     <citations>