diff add_protein_features.xml @ 9:0b46a7aead62 draft

planemo upload commit eb7450f36863f02f036cbc52bf5525d68f22bd9e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_protein_features.xml	Tue Dec 18 08:26:55 2018 -0500
@@ -0,0 +1,163 @@
+<tool id="prot_features" name="Add protein features" version="2018.12.18">
+<description>[neXtProt]
+</description>
+<requirements>
+  <requirement type="package" version="3.4.1">R</requirement>
+</requirements>
+<stdio>
+  <exit_code range="1:" />
+</stdio>
+<command><![CDATA[
+
+  Rscript $__tool_directory__/add_protein_features.R 
+  --inputtype="$inputtype.filetype"
+  --input='$inputtype.genelist'
+
+  #if $inputtype.filetype == "file" 
+    --column='$inputtype.column' 
+    --header=$inputtype.header
+  #end if
+
+  --type='$idtype'
+  --pc_features='$Nextprot_params.pc_features' 
+  --localization='$Nextprot_params.localization' 
+  --diseases_info='$Nextprot_params.diseases_info'  
+  --output='$output'  
+  --nextprot=$__tool_directory__/tool-data/result_nextprot.txt 
+    
+]]></command>
+
+<inputs>
+  <conditional name="inputtype">
+    <param name="filetype" type="select" label="Enter your IDs (neXtProt or UniProt)" 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>
+    <when value="copy_paste">
+      <param name="genelist" type="text" label="Enter a list of IDs separated by tab, space or carriage return into the form field" help="for example : A0AVI2 A6NGB0">
+        <sanitizer invalid_char="">
+            <valid initial="string.printable">
+                <remove value="&apos;"/>
+            </valid>
+            <mapping initial="none">
+                <add source="&apos;" target="__sq__"/>
+                <add source="&#x20;" target=""/>
+                <add source="&#xA;" target=""/>
+                <add source="&#xD;" target=""/>
+                <add source="&#x9;" target=""/>
+            </mapping>
+        </sanitizer>
+      </param>
+    </when>
+    <when value="file">
+      <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
+      <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1"/> 
+      <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" />
+
+    </when>
+  </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>
+      </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="true"> 
+          <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="diseases_info" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Disease information" />
+
+      </section>
+
+</inputs>
+
+
+<outputs>
+  <data name="output" format="tsv" label="Add_information_from_neXtProt on ${inputtype.genelist.name}">
+    <filter>inputtype=="file"</filter>
+  </data>
+  <data name="output" format="tsv" label="Add_information_from_neXtProt"/>
+</outputs>
+
+<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="column" value="c1"/>
+      <param name="header" value="true"/>
+    </conditional>
+
+    <param name="idtype" value="uniprot"/> 
+
+    <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>
+      
+    <output name="output" file="Add_information_from_neXtProt.tsv"/>
+  </test>
+</tests>
+
+<help><![CDATA[
+
+**Description**
+
+This tool retrieves annotation (protein features) from the neXtProt database (knowledgebase on human proteins) to enrich your protein IDs list.
+
+-----
+
+**Input**
+
+A list of of Uniprot (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.  
+
+-----
+
+**Parameters**
+
+"Select fetures": 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. 
+
+-----
+
+**Output**
+
+Output is a tabular file containing both original columns and new columns including the annotation requested.  
+
+-----
+
+**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)
+
+using a REST API (https://academic.oup.com/nar/article/43/D1/D764/2439066#40348985) (Gaudet et  al., 2017)
+
+-----
+
+.. class:: infomark
+
+**Authors**
+
+David Christiany, Lisa Peru, 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
+
+This work has been partially funded through the French National Agency for Research (ANR) IFB project.
+
+Contact [e-mail] for any questions or concerns about the Galaxy implementation of this tool.
+ 
+    ]]></help>
+    <citations>
+    </citations>
+
+</tool>