diff add_expression_data.xml @ 14:133309fd6875 draft

"planemo upload commit c4edbc8a0ffd86395f088cb5b6592f77db658ac7"

--- a/add_expression_data.xml	Fri Jun 28 05:01:37 2019 -0400
+++ b/add_expression_data.xml	Fri Jan 24 04:22:48 2020 -0500
@@ -1,28 +1,41 @@
-<tool id="rna_abbased_data" name="Add expression data" version="2019.06.27">
+<tool id="rna_abbased_data" name="Add expression data" version="2020.01.24">
 <description> (RNAseq or Immuno-assays)[Human Protein Atlas]
 </description>
 <requirements>
-  <requirement type="package" version="3.4.1">R</requirement>
+  <requirement type="package" version="3.4.4">R</requirement>
 </requirements>
 <stdio>
   <exit_code range="1:" />
 </stdio>
 <command><![CDATA[
 
-  #if $inputtype.filetype == "copy_paste": 
-  
-    Rscript $__tool_directory__/add_expression_HPA.R --inputtype="copypaste" --input='$inputtype.genelist' --atlas="$__tool_directory__/proteinatlas.csv" --select='$options.hpaparams' --output='$output'  
+    Rscript $__tool_directory__/add_expression_HPA.R
+    --input='$inputtype.genelist'
+    --select='$options.hpaparams'
+    --output='$output' 
+    
+    #if $inputtype.filetype == "copy_paste": 
+        --inputtype="copypaste"    
+    #else 
+        --inputtype="tabfile" 
+        --header='$inputtype.header' 
+        --column='$inputtype.column'  
+    #end if
 
-  #else 
-  
-    Rscript $__tool_directory__/add_expression_HPA.R --inputtype="tabfile" --input='$inputtype.genelist' --header='$inputtype.header' --atlas="$__tool_directory__/proteinatlas.csv" --column='$inputtype.column' --select='$options.hpaparams' --output='$output'  
-
-  #end if
-   
+    #if "protein_atlas" in str($ref_file).split("/")
+    --atlas="$ref_file"
+    #else 
+    --atlasf="$__tool_directory__/$ref_file"
+    #end if
 
 ]]></command>
 
 <inputs>
+    <param name="ref_file" type="select" label="HPA source file version" >
+        <options from_data_table="proteore_protein_full_atlas">
+            <filter type="sort_by" column="0"/>
+        </options>
+    </param>
   <conditional name="inputtype">
     <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>
@@ -54,12 +67,12 @@
           <option value="Gene description" selected="false">Gene description</option>
           <option value="Evidence">Evidence (at protein level, at transcript level or no evidence)</option>
           <option value="Antibody">Antibody reference</option>
-          <option value="RNA tissue category">RNA tissue category</option>
- 		      <option value="Reliability (IH)">IH detection level</option>
+          <option value="RNA tissue specificity">RNA tissue category</option>
+ 		  <option value="Reliability (IH)">IH detection level</option>
           <option value="Reliability (IF)">IF detection level</option>
           <option value="Subcellular location">Subcellular location</option>
-          <option value="RNA TS TPM">RNA tissue specificity abundance in 'Transcript Per Million'</option>
-          <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million'</option>
+          <option value="RNA tissue specific NX">RNA tissue specificity abundance in 'Transcript Per Million'</option>
+          <option value="TPM max in non-specific">RNA non-specific tissue abundance in 'Transcript Per Million' (only for 23/10/2018 release)</option>
     </param>
   </section>
 
@@ -124,7 +137,7 @@
 
 - RNA tissue specificity abundance in 'Transcript Per Million': For each gene is reported the tissue specificity abundance in 'Transcript Per Million' (TPM) as the sum of the TPM values of all its protein-coding transcripts.
 
-- RNA non-specific tissue abundance in 'Transcript Per Million': please refer to http://www.proteinatlas.org/about/assays+annotation#rna.
+- RNA non-specific tissue abundance in 'Transcript Per Million' (only available from 23/10/2018 release): please refer to http://www.proteinatlas.org/about/assays+annotation#rna.
 
 -----
 
@@ -134,9 +147,13 @@
 
 -----
 
-**Data sources (release date)**
+**HPA source file version (release date)**
+
+Release date 23/10/2018: data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38
 
-HPA source file (data are based on the Human Protein Atlas version 18.1 and Ensembl version 88.38):  http://www.proteinatlas.org/download/proteinatlas.tab.gz
+Release date 21/01/2020: a subset of the data in the Human Protein Atlas version 19.1
+
+downloaded from:  http://www.proteinatlas.org/download/proteinatlas.tab.gz
 
 -----