Mercurial > repos > proteore > proteore_tissue_specific_expression_data

changeset 1:7adaf6ac15c1 draft

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"planemo upload commit aeaa0ae28d6b8a3a5e46b926b771bd7f3b23910f-dirty"
author proteore
date Wed, 22 Jan 2020 13:43:22 +0000
parents 3029dd9992fb
children 9d10be16f371
files Build_tissue-specific_expression_dataset.xml
diffstat 1 files changed, 19 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/Build_tissue-specific_expression_dataset.xml	Thu Jun 27 04:05:07 2019 -0400
+++ b/Build_tissue-specific_expression_dataset.xml	Wed Jan 22 13:43:22 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="retrieve_from_hpa" name="Build tissue-specific expression dataset" version="2019.06.27">
+<tool id="retrieve_from_hpa" name="Build tissue-specific expression dataset" version="2020.01.22">
 <description>[Human Protein Atlas](no input required)</description>
 <requirements>
   <requirement type="package" version="3.4.1">R</requirement>
@@ -10,15 +10,21 @@
   $__tool_directory__/Build_tissue-specific_expression_dataset.R
   --data_source="$input.data_source"
   #if $input.data_source == "IHC"
-    --hpa_ref="$__tool_directory__/normal_tissue.tsv"
     --tissue="$input.normal_tissue"
     --level="$input.level"
     --reliability="$input.reliability"
   #else if $input.data_source == "RNAseq"
-    --hpa_ref="$__tool_directory__/rna_tissue.tsv"
     --sample="$input.sample"
   #end if
+  
+  #if "protein_atlas" in str($input.ref_file).split("/")
+    --hpa_ref="$input.ref_file"
+  #else 
+    --hpa_ref="$__tool_directory__/$input.ref_file"
+  #end if
+  
   --output="$output"
+
 </command>
 
 <inputs>
@@ -28,6 +34,11 @@
     <option value="RNAseq">RNA levels based on RNA-seq experiments</option>
   </param>
   <when value="IHC">
+    <param name="ref_file" type="select" label="Release" >
+        <options from_data_table="proteore_protein_atlas_normal_tissue">
+            <filter type="sort_by" column="0"/>
+        </options>
+    </param>
     <param name="normal_tissue" type="select" label="Select tissue (by clicking in the box)" multiple="True" optional="False">
       <option value="adrenal gland" >Adrenal gland</option>
       <option value="appendix" >Appendix</option>
@@ -93,6 +104,11 @@
     </param>
   </when>
   <when value="RNAseq">
+    <param name="ref_file" type="select" label="Release" >
+        <options from_data_table="proteore_protein_atlas_tumor_tissue">
+            <filter type="sort_by" column="0"/>
+        </options>
+    </param>
     <param name="sample" type="select" label="Select tissue (by clicking in the box)" multiple="True" optional="False">
       <option value="adipose tissue">Adipose tissue</option>
       <option value="adrenal gland">Adrenal gland</option>