diff add_protein_features_mouse.xml @ 0:1e856941a888 draft

planemo upload commit 8de59a5dbf9206fa3d9f7a1c07e79ccb792b3e3f-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_protein_features_mouse.xml	Fri Feb 08 08:46:04 2019 -0500
@@ -0,0 +1,150 @@
+<tool id="prot_features_mouse" name="Add protein features (Mouse)" version="2019.02.08">
+<description>[UniProt]
+</description>
+<requirements>
+  <requirement type="package" version="3.4.1">R</requirement>
+</requirements>
+<stdio>
+  <exit_code range="1:" />
+</stdio>
+<command><![CDATA[
+
+  Rscript $__tool_directory__/add_protein_features_mouse.R 
+  --inputtype="$inputtype.filetype"
+  --input='$inputtype.genelist'
+
+  #if $inputtype.filetype == "file" 
+    --column='$inputtype.column' 
+    --header=$inputtype.header
+  #end if
+
+  --pc_features='$pc_features'   
+  --output='$output'  
+  --uniprot_file=$__tool_directory__/tool-data/uniprot_features_mouse.tsv
+    
+]]></command>
+
+<inputs>
+  <conditional name="inputtype">
+    <param name="filetype" type="select" label="Enter your IDs (UniProt-AC)" 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="">
+        <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="pc_features" type="select" label="Features/Annotation" multiple="true" help="" display="checkboxes" optional="true">
+      <option value="Entry name" selected="false">Entry name (e.g. PLK3_MOUSE)</option>
+      <option value="Protein names" selected="false">Protein names (e.g. Serine/threonine-protein kinase PLK3 (EC 2.7.11.21))</option>
+      <option value="Length" selected="false">Sequence length</option>
+      <option value="Mass" selected="false">Molecular Mass (Da)</option>
+      <option value="Features" selected="false">Features (e.g. Chain (1); Transmembrane (4))</option>
+      <option value="Intramembrane" selected="false">Intramembrane (e.g. INTRAMEM 104 116 Helical; Name=Pore helix 1. {ECO:0000250|UniProtKB:O00180})</option>
+      <option value="Transmembrane" selected="false">Transmembrane (e.g. TRANSMEM 1 21 Helical. {ECO:0000255})</option>
+      <option value="Topological domain" selected="false">Topological domain (e.g. TOPO_DOM 33 64 Extracellular. {ECO:0000250|UniProtKB:P11169})</option>
+      <option value="Pathway" selected="false">Pathway (e.g. Steroid metabolism; cholesterol metabolism)</option>
+      <option value="Function [CC]" selected="false">Function (e.g. FUNCTION: Serine/threonine-protein kinase involved in cell cycle regulation)</option>
+      <option value="Post-translational modification" selected="false">Post-translational modification (e.g. PTM: Phosphorylation on Ser-300 or Ser-302 and on Ser-420)</option>
+      <option value="Subcellular location [CC]" selected="false">Subcellular location (e.g. SUBCELLULAR LOCATION: Secreted)</option>
+      <option value="Subunit structure [CC]" selected="false">Subunit structure (e.g. SUBUNIT: Homodimer. Heterodimerizes with YWHAE (By similarity))</option>
+      <option value="Domain [CC]" selected="false">Domain (e.g. DOMAIN: The Walker motif (consensus sequence G-X-X-G-X-G-K-[ST]-T) is expected to bind ATP)</option>
+      <option value="Tissue specificity" selected="false">Tissue specificity (e.g. TISSUE SPECIFICITY: Highest expression in fat cells {ECO:0000269|PubMed:7629182})</option>
+      <option value="Involvement in disease" selected="false">Involvement in disease (e.g. DISEASE: Note=Defects in Btk are the cause of murine X-linked immunodeficiency (XID))</option>     
+    </param>
+</inputs>
+
+<outputs>
+  <data name="output" format="tsv" label="Add_information_from_UniProt on ${inputtype.genelist.name}">
+    <filter>inputtype=="file"</filter>
+  </data>
+  <data name="output" format="tsv" label="Add_information_from_UniProt"/>
+</outputs>
+
+<tests>
+  <test>
+    <conditional name="inputtype">
+      <param name="filetype " value="file"/>
+      <param name="genelist" value="Wilson-foie-souris-up.txt"/>
+      <param name="column" value="c1"/>
+      <param name="header" value="true"/>
+    </conditional>
+
+    <param name="pc_features" value='Entry name,Protein names,Length,Mass,Features,Intramembrane,Transmembrane,Topological domain,Pathway,Function [CC],Post-translational modification,Subcellular location [CC],Subunit structure [CC],Domain [CC],Tissue specificity,Involvement in disease'/> 
+      
+    <output name="output" file="results_wilson-foie-souris-up.tsv"/>
+  </test>
+</tests>
+
+<help><![CDATA[
+
+**Description**
+
+This tool retrieves annotation (protein features) from the UniProt database (Mouse proteins) to enrich your protein IDs list.
+
+-----
+
+**Input**
+
+A list of Uniprot Accession Number (e.g. P05090) entered in a copy/paste mode or a file containing one or multiple columns with **at least one column of Uniprot accession number**. If your input file contains other type of IDs, please use the ID_Converter tool.  
+
+-----
+
+**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. 
+
+You can get more information about annotations `here <https://www.uniprot.org/help/uniprotkb_column_names>`_.
+
+
+-----
+
+**Output**
+
+Output is a tabular file containing both original columns and new columns including the annotation requested.  
+Please, note that a "NA" is returned when there is no information available from UniProt.
+
+-----
+
+**Data source (release date)**
+
+Annotations have been retrieved from UniProt.org (02/2019).
+
+-----
+
+.. 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>