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Changeset 6:6cb20e130473 (2023-09-28)

Previous changeset 5:f9db47f68e5e (2023-04-07) Next changeset 7:7d87a9d58aa1 (2023-10-03)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3ac2b4221e3aa5de4cef9f453ac1a7425ce130c2

modified:
pyega3.xml
test-data/filelist_EGAD00001003338.tabular

added:
README.rst

removed:
README.md

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