diff add_protein_features.xml @ 18:0a9ae3d7dbf2 draft default tip

"planemo upload commit 7afd4b3ee25f024257ccbac6e51076d25b2a04e7"

--- a/add_protein_features.xml	Fri Jan 24 05:04:15 2020 -0500
+++ b/add_protein_features.xml	Thu Aug 20 03:09:52 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="prot_features" name="Add protein features" version="2020.01.23">
+<tool id="prot_features" name="Add protein features" version="2020.08.17">
 <description>[neXtProt, Human]
 </description>
 <requirements>
@@ -19,9 +19,7 @@
   #end if
 
   --type='$idtype'
-  --pc_features='$Nextprot_params.pc_features' 
-  --localization='$Nextprot_params.localization' 
-  --diseases_info='$Nextprot_params.diseases_info'  
+  --pc_features='$pc_features' 
   --output='$output'  
 
   #if 'proteore_nextprot_ref' in str($ref_file).split("/")
@@ -63,32 +61,31 @@
     </when>
   </conditional>
 
-      <param name="idtype" type="select" label="Type of IDs" multiple="false" optional="false"> 
-            <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 (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="idtype" type="select" label="Type of IDs" multiple="false" optional="false"> 
+        <option value="NextprotID" selected="true">neXtProt IDs</option>
+        <option value="Uniprot_AC" selected="false">UniProt accession number</option>
+    </param>
+    <param name="pc_features" type="select" label="Features/Annotation" multiple="true" help="" display="checkboxes" optional="false">
+        <option value="ProteinName" selected="false">Protein name</option>
+	    <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="SubcellLocations" selected="false">Subcellular Location</option>
+        <option value="Diseases" selected="false">Disease information</option>
+        <option value="Function" selected="false">Protein function</option>
+        <option value="PostTranslationalModifications" selected="false">Post translational modifications</option>
+        <option value="ProteinFamily" selected="false">Protein family</option>
+        <option value="Pathway" selected="false">Pathway(s)</option>
+	    <option value="ProteinExistence" selected="false">Protein Existence (evidence score from 1 to 5)</option>
+        <option value="Chr" selected="false">Chromosome</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="true" truevalue="true" falsevalue="false" label="Disease information" />
-
-      </section>
-      <param name="ref_file" type="select" label="Release of neXtProt reference file to use">
+    <param name="ref_file" type="select" label="Release of neXtProt reference file to use">
         <options from_data_table="proteore_nextprot_ref">
             <filter type="sort_by" column="0"/>
         </options>
-      </param>
+    </param>
 
 </inputs>
 
@@ -110,12 +107,7 @@
     </conditional>
 
     <param name="idtype" value="Uniprot_AC"/> 
-
-    <section name="Nextprot_params">
-      <param name="pc_features" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/> 
-      <param name="localization" value="Chr,SubcellLocations"/> 
-      <param name="diseases_info" value="true"/> 
-    </section>
+    <param name="pc_features" value="SeqLength,MW,IsoPoint,TMDomains,ProteinExistence"/> 
       
     <param name="ref_file" value="test-data/cached_locally/nextprot_ref_07-05-2019.tsv"/>
     <output name="output" file="Add_information_from_neXtProt.tsv"/>
@@ -126,7 +118,7 @@
 
 **Description**
 
-This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich your protein IDs list.
+This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich and better inform your protein IDs list.
 
 -----
 
@@ -148,7 +140,11 @@
 
 **Output**
 
-Output is a tabular file containing both original columns and new columns including the annotation requested.  
+Output is a tabular file containing both original columns and new columns including the annotation requested. Only features/annotations assigned with a "GOLD" quality criterion are considered, otherwise a "NA" value is returned.
+
+.. class:: warningmark
+
+"Protein name","Protein function","Post translational modifications","Protein family","Pathway(s)" options will not work will releases older than 08/2020.
 
 -----
 
@@ -158,16 +154,21 @@
 
  neXtProt releases : 
  
-- nextProt release 07-05-2019 (release Feb 13, 2019)
-- neXtProt release 08-10-2018 (release Feb 21, 2018)
+- nextProt release 31-07-2020 (release Feb, 2020)
+- nextProt release 07-05-2019 (release Feb, 2019)
+- neXtProt release 08-10-2018 (release Feb, 2018)
   
+.. class:: warningmark
+
+For "Protein function", "Post translational modifications" and "Pathway(s)", only results with gold quality are returned.
+
 -----
 
 .. class:: infomark
 
 **Authors**
 
-David Christiany, Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+David Christiany, Lisa Perus, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
 
 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR