diff add_expression_data.xml @ 12:dbeabf9bf091 draft

planemo upload commit 51fc514a85c1055cab5bb6e76c90f3da7e648101-dirty

--- a/add_expression_data.xml	Wed Jan 02 04:40:04 2019 -0500
+++ b/add_expression_data.xml	Thu Mar 07 09:08:33 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="rna_abbased_data" name="Add expression data" version="2019.01.02">
+<tool id="rna_abbased_data" name="Add expression data" version="2019.03.07">
 <description> (RNAseq or Immuno-assays)[Human Protein Atlas]
 </description>
 <requirements>
@@ -24,7 +24,7 @@
 
 <inputs>
   <conditional name="inputtype">
-    <param name="filetype" type="select" label="Enter your IDs (Ensembl gene ENSG IDs only)" help="Copy/paste or from a file (e.g. table)"> 
+    <param name="filetype" type="select" label="Enter your IDs (Ensembl gene IDs only, e.g. ENSG00000064787)" help="Copy/paste or from a file (e.g. table)"> 
       <option value="file_all" selected="true">Input file containing your IDs</option>
       <option value="copy_paste">Copy/paste your list of IDs</option> 
     </param>
@@ -42,11 +42,10 @@
     </when>
     <when value="file_all">
       <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 if ENSG ID are in column n°1)" value="c1"/> 
-      <param name="header" type="select" label="Does file contain header?" multiple="false" optional="false"> 
- 		      <option value="true" selected="true">Yes</option>
-          <option value="false" selected="false">No</option>
+      <param name="column" type="text" label="Column IDs (e.g : Enter c1 if ENSG ID are in column n°1)" value="c1">
+        <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
       </param>
+      <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?"/>
     </when>
   </conditional>
   <section name="options" title="RNAseq/Ab-based expression data" expanded="True">   
@@ -95,7 +94,7 @@
 
 **Input**
 
-Input can be either a list of Ensembl gene (ENSG) IDsds (copy/paste mode) or a file containing multiple fields with at least one column of Ensembl gene IDs. If your input file contains other type of IDs, please use the ID_Converter tool to create a column of Ensembl gene IDs.  
+Input can be either a list of Ensembl gene (ENSG) IDs (copy/paste mode) or a file containing multiple fields with at least one column of Ensembl gene IDs. If your input file contains other type of IDs, please use the ID_Converter tool to create a column of Ensembl gene IDs.  
 
 -----
 
@@ -127,13 +126,13 @@
 
 **Output**
 
-The output is a tabular file containing original columns and new columns including selected annotation.  
+The output is a tabular file containing initial columns and new columns with annotation from HPA.  
 
 -----
 
 **Data sources (release date)**
 
-HPA source file (Human Protein Atlas version 18):  http://www.proteinatlas.org/download/proteinatlas.tab.gz
+HPA source file (Human Protein Atlas version 18.1):  http://www.proteinatlas.org/download/proteinatlas.tab.gz
 
 -----
 
@@ -141,7 +140,7 @@
 
 **Authors**
 
-Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+Lisa Peru, David Christiany, 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