changeset 2:3e65e0249976 draft

planemo upload commit 12b0b3e18cd7af9a8588906fa2ec199b9d2a770f-dirty

--- a/Build_tissue-specific_expression_dataset.R	Tue Dec 18 08:33:26 2018 -0500
+++ b/Build_tissue-specific_expression_dataset.R	Fri Mar 01 08:06:59 2019 -0500
@@ -15,8 +15,6 @@
   return(res.imm)
 }
 
-    
-    
 select_HPARNAseq<-function(hpa_ref, sample) {
   HPA.rnaTissue = read.table(hpa_ref,header=TRUE,sep="\t",stringsAsFactors = FALSE)
   res.rna <- subset(HPA.rnaTissue, Sample%in%sample, select = -c(Unit))
@@ -34,13 +32,13 @@
   if("--help" %in% args) {
     cat("Selection and Annotation HPA
     Arguments:
-        --data_source: immuno/rnaseq
+        --data_source: IHC/RNAseq
         --hpe_ref: path to reference file normal_tissue.tsv/rna_tissue.tsv)
-          if immuno:
+          if IHC:
             --tissue: list of tissues
             --level: Not detected, Low, Medium, High
             --reliability: Supported, Approved, Enhanced, Uncertain
-          if rnaseq:
+          if RNAseq:
             --sample: Sample tissues 
         --output: output filename \n")
     q(save="no")
@@ -55,17 +53,17 @@
   # Extract options
   data_source = args$data_source
   hpa_ref = args$hpa_ref
-  if (data_source == "immuno") {
+  if (data_source == "IHC") {
     tissue = strsplit(args$tissue, ",")[[1]]
     level = strsplit(args$level, ",")[[1]]
     reliability = strsplit(args$reliability, ",")[[1]]
     # Calculation
-    res = select_HPAimmunohisto(hpa_ref, tissue, level, reliability)
+    res = suppressWarnings(select_HPAimmunohisto(hpa_ref, tissue, level, reliability))
   }
-  else if (data_source == "rnaseq") {
+  else if (data_source == "RNAseq") {
     sample = strsplit(args$sample, ",")[[1]]
     # Calculation
-    res = select_HPARNAseq(hpa_ref, sample)
+    res = suppressWarnings(select_HPARNAseq(hpa_ref, sample))
   }
 
   # Write output

--- a/Build_tissue-specific_expression_dataset.xml	Tue Dec 18 08:33:26 2018 -0500
+++ b/Build_tissue-specific_expression_dataset.xml	Fri Mar 01 08:06:59 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="retrieve_from_hpa" name="Build tissue-specific expression dataset" version="2018.12.12">
+<tool id="retrieve_from_hpa" name="Build tissue-specific expression dataset" version="2019.02.27">
 <description>[Human Protein Atlas](no input required)</description>
 <requirements>
   <requirement type="package" version="3.4.1">R</requirement>
@@ -9,12 +9,12 @@
 <command interpreter="Rscript">
   $__tool_directory__/Build_tissue-specific_expression_dataset.R
   --data_source="$input.data_source"
-  #if $input.data_source == "immuno"
+  #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"
+  #else if $input.data_source == "RNAseq"
     --hpa_ref="$__tool_directory__/rna_tissue.tsv"
     --sample="$input.sample"
   #end if
@@ -24,10 +24,10 @@
 <inputs>
 <conditional name="input">
   <param name="data_source" type="select" label="Experimental data source (antibody- or RNAseq-based)">
-    <option value="immuno">Expression profiles based on immunohistochemistry</option>
-    <option value="rnaseq">RNA levels based on RNA-seq experiments</option>
+    <option value="IHC">Expression profiles based on immunohistochemistry</option>
+    <option value="RNAseq">RNA levels based on RNA-seq experiments</option>
   </param>
-  <when value="immuno">
+  <when value="IHC">
     <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>
@@ -92,7 +92,7 @@
 
     </param>
   </when>
-  <when value="rnaseq">
+  <when value="RNAseq">
     <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>
@@ -137,13 +137,13 @@
 </inputs>
 
 <outputs>
-  <data name="output" format="tsv" label=""/>
+  <data name="output" format="tsv" label="Tissue-specific_expression_from_${input.data_source}"/>
 </outputs>
 
 <tests>
   <test>
     <conditional name="input">
-      <param name="data_source" value="immuno"/>
+      <param name="data_source" value="IHC"/>
       <param name="normal_tissue" value="lung,ovary"/>
       <param name="level" value="High"/>
       <param name="reliability" value="Approved,Supported"/>