# HG changeset patch
# User ebi-gxa
# Date 1609027219 0
# Node ID c3c85b67d11869800cd2da997a4651dfb902c8a7
# Parent  2e81fbe036b20e2b9e2d60bcd637db78942d0001
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 81ed2d7aaad0f5536d835e75e483c39c3984d565"

diff -r 2e81fbe036b2 -r c3c85b67d118 matrix-service.xml
--- a/matrix-service.xml	Tue Oct 22 11:03:12 2019 -0400
+++ b/matrix-service.xml	Sun Dec 27 00:00:19 2020 +0000
@@ -1,13 +1,16 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="hca_matrix_downloader" name="Human Cell Atlas Matrix Downloader" version="v0.0.3+galaxy0">
+<tool id="hca_matrix_downloader" name="Human Cell Atlas Matrix Downloader" version="v0.0.4+galaxy0">
   <description>retrieves expression matrices and metadata from the Human Cell Atlas.</description>
   <requirements>
-    <requirement type="package" version="0.0.3">hca-matrix-downloader</requirement>
+    <requirement type="package" version="0.0.4">hca-matrix-downloader</requirement>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
 
 hca-matrix-downloader -p '${project}' -o out -f '${matrix_format}'
 
+#if $species:
+  -s ${species}
+#end if
 #if $matrix_format == "mtx":
   && hca-mtx-to-10x out.mtx .
   && gunzip -c out.mtx/cells.tsv.gz > exp_design.tsv
@@ -21,6 +24,7 @@
       <option value="mtx" selected="true">Matrix Market</option>
       <option value="loom">Loom</option>
     </param>
+    <param name="species" argument="--species" optional="true" type="text" label="Species to use" help="Certain studies will contain more than one species, in that case, one should be given as input. If you try to download data from such a study, the tool will fail and give you a list in the Std. out of what are the potential species to paste here. This is not needed for most studies that have a single species."/>
   </inputs>
 
   <outputs>
@@ -43,12 +47,18 @@
 
   <tests>
     <test>
-      <param name="project" value="Single cell transcriptome analysis of human pancreas"/>
+      <param name="project" value="cddab57b-6868-4be4-806f-395ed9dd635a"/>
       <param name="matrix_format" value="mtx"/>
-      <output name="matrix_mtx" file="matrix.mtx" ftype="txt"/>
-      <output name="genes_tsv" file="genes.tsv" ftype="tsv"/>
-      <output name="barcode_tsv" file="barcodes.tsv" ftype="tsv"/>
-      <output name="cells_meta_tsv" file="exp_design.tsv" ftype="tsv"/>
+      <output name="matrix_mtx" md5="0549fc0260eb6974affb115ac80b6e85" ftype="txt"/>
+      <output name="genes_tsv" md5="7e131ba105f713d2f9766d61c246d0da" ftype="tsv"/>
+      <output name="barcode_tsv" md5="327926a684ad8eaee5de8243c32b415c" ftype="tsv"/>
+      <output name="cells_meta_tsv" md5="defa674847e3e1877ab1957a3291b28d" ftype="tsv"/>
+    </test>
+    <test>
+      <param name="project" value="f8aa201c-4ff1-45a4-890e-840d63459ca2"/>
+      <param name="matrix_format" value="loom"/>
+      <param name="species" value="homo_sapiens"/>
+      <output name="matrix_loom" md5="9ba6bd109ec271c338251c5519ea9f5d" ftype="h5"/>
     </test>
   </tests>
 
@@ -61,9 +71,13 @@
 and metadata for any public experiment available at Human Cell Atlas data portal.
 
 To use it, simply set the name, or label, or ID for the desired project, which can be
-found at the HCA data browser (https://prod.data.humancellatlas.org/explore/projects),
+found at the HCA data browser (https://data.humancellatlas.org/explore/projects),
 and select the desired matrix format (Matrix Market or Loom).
 
+For projects that have more than one organism, one needs to be specified. If none
+is specified, then the job will fail and the available options to be specified
+will be listed in the stdout of the job.
+
 Outputs will be:
 
 - *When "Matrix Market" is seleted, outputs are in 10X-compatible Matrix Market format:*
@@ -98,11 +112,14 @@
 
 **Version history**
 
+     0.0.4+galaxy0: Retrieves data from EBI FTP until an equivalent Matrix service for DCP 2.0 is established. Deals with multi organisms studies.
+
      0.0.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Teichmann Lab at Wellcome Sanger Institute and
      Expression Atlas team https://www.ebi.ac.uk/gxa/home  at EMBL-EBI https://www.ebi.ac.uk/.
 
 ]]></help>
   <citations>
     <citation type="doi">10.7554/eLife.27041</citation>
+    <citation type="doi">10.1101/2020.04.08.032698</citation>
   </citations>
 </tool>