# HG changeset patch
# User iuc
# Date 1695902836 0
# Node ID 6cb20e1304734d746ea8ac93bae8ac4f675a21a6
# Parent  f9db47f68e5ecc6ff1e1f8e6cd7141c59492f1fd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3ac2b4221e3aa5de4cef9f453ac1a7425ce130c2

diff -r f9db47f68e5e -r 6cb20e130473 README.md
--- a/README.md	Fri Apr 07 21:48:18 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-# PyEGA3
-
-## Set up user credentials on Galaxy
-
-To enable users to set their credentials for this tool,
-make sure the file `config/user_preferences_extra.yml` has the following section:
-
-```
-    ega_account:
-        description: Your EGA (European Genome Archive) account
-        inputs:
-            - name: username
-              label: Username
-              type: text
-              required: False
-            - name: password
-              label: Password
-              type:  password
-              required: False
-```
diff -r f9db47f68e5e -r 6cb20e130473 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Sep 28 12:07:16 2023 +0000
@@ -0,0 +1,22 @@
+PyEGA3
+======
+
+Set up user credentials on Galaxy
+---------------------------------
+
+To enable users to set their credentials for this tool, make sure the
+file ``config/user_preferences_extra.yml`` has the following section:
+
+::
+
+       ega_account:
+           description: Your EGA (European Genome Archive) account
+           inputs:
+               - name: username
+                 label: Username
+                 type: text
+                 required: False
+               - name: password
+                 label: Password
+                 type:  password
+                 required: False
diff -r f9db47f68e5e -r 6cb20e130473 pyega3.xml
--- a/pyega3.xml	Fri Apr 07 21:48:18 2023 +0000
+++ b/pyega3.xml	Thu Sep 28 12:07:16 2023 +0000
@@ -234,6 +234,12 @@
     <help><![CDATA[
 The pyEGA3 download client is a python-based tool for viewing and downloading files from authorized EGA datasets.
 
+.. class:: Warning mark
+
+	Data is stored unencrypted on the user's Galaxy account. Confidential data from the EGA could be left unprotected when uploaded to a public Galaxy server.
+	Make sure to read the EGA Data Access Agreement ([DAA](https://ega-archive.org/files/Example_DAA.doc)) before uploading any data to Galaxy from the EGA.
+	If this applies to you, we recommend you follow [this link](https://github.com/elixir-europe/GalaxySensitiveData-ELIXIR_IS) for updates on encrypted data at rest.
+
 If you have an EGA account, you can set your EGA credentials in the user preferences menu of Galaxy. Otherwise, default EGA credentials with access to an example dataset will be used.
 
 pyEGA3 uses the EGA Data API and has several key features:
diff -r f9db47f68e5e -r 6cb20e130473 test-data/filelist_EGAD00001003338.tabular
--- a/test-data/filelist_EGAD00001003338.tabular	Fri Apr 07 21:48:18 2023 +0000
+++ b/test-data/filelist_EGAD00001003338.tabular	Thu Sep 28 12:07:16 2023 +0000
@@ -81,3 +81,7 @@
 EGAF00007553559	1	2426228900	66bb08a031ff66c8c03ee9917be53fcf	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.genotypes_only_chr1and2.vcf.gz
 EGAF00007553560	1	2691732	26d41f1a09671c834fd7b4eaac3f1a67	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.genotypes.vcf.gz.tbi
 EGAF00007553561	1	434009	357abb1556367d5c096cd54801a5e783	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.genotypes_only_chr1and2.vcf.gz.tbi
+EGAF00008047669	1	14585114453	1377526fc26a58294635ba48edc35535	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.redo.genotypes.bcf
+EGAF00008047670	1	2260066	638b9524583d585c5276eed6e1f198b0	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.redo.genotypes.bcf.csi
+EGAF00008047671	1	2053513514	a6d323bb194eac03e7112c243aeef5d3	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.redo.genotypes_only_chr1and2.bcf
+EGAF00008047672	1	353029	ae95e52511a6a28b9b01d2beabdc59dd	EE-2564.ALL_2504_Samples.wgs.phase3.v5.20130502.redo.genotypes_only_chr1and2.bcf.csi