# HG changeset patch
# User ebi-gxa
# Date 1565688972 14400
# Node ID cc21614b6693ff6322e107041086d583dc69101a
# Parent  cd6b80f62fcc58144a58baf37fc30383a6228943
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 7bf75360bdf687f987e706c3e48667931eaed0ce-dirty

diff -r cd6b80f62fcc -r cc21614b6693 retrieve-scxa.xml
--- a/retrieve-scxa.xml	Wed Apr 03 12:01:53 2019 -0400
+++ b/retrieve-scxa.xml	Tue Aug 13 05:36:12 2019 -0400
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="retrieve_scxa" name="EBI SCXA Data Retrieval" version="v0.0.1+galaxy1">
+<tool id="retrieve_scxa" name="EBI SCXA Data Retrieval" version="v0.0.2+galaxy2">
   <description>Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA)</description>
   <requirements>
-    <requirement type="package" version="1.18">gnu-wget</requirement>
+    <requirement type="package" version="1.20.1">wget</requirement>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
 
@@ -19,8 +19,8 @@
 
 wget -O ${matrix_mtx} 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.mtx';
 wget -qO - 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.mtx_cols' | cut -f2 > ${barcode_tsv};
-wget -qO - 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.mtx_rows'
- | awk '{OFS="\t"; print \$2,\$2}' > ${genes_tsv};
+wget -qO - 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.decorated.mtx_rows' |
+  awk -F'\t' '{ if (length($2) == 0) { print $1"\t"$1 } else { print $0 } }' > ${genes_tsv};
 
 #end if
 
@@ -88,6 +88,7 @@
   already normalized/scaled. You should keep this in mind when using this data
   on methods that will try to normalise data as part of their procedure. Due to technical
   particularities in the current Atlas SC pipeline, TPMs available here are not filtered.
+  **Note: droplet databases won't have TPM data**
 
 Outputs will be: