Mercurial > repos > iuc > ena_upload

changeset 14:5cb6146337d8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ab38fa3d5ec06729c1efa86240ec57b8143b21ed
author iuc
date Wed, 12 Jun 2024 16:01:11 +0000
parents ea5e944f447d
children
files ena_upload.xml samples_macros.xml
diffstat 2 files changed, 6 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/ena_upload.xml	Wed Mar 27 16:46:55 2024 +0000
+++ b/ena_upload.xml	Wed Jun 12 16:01:11 2024 +0000
@@ -1,7 +1,7 @@
 <tool id="ena_upload" name="ENA Upload tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05" license="MIT">
     <description>Submission of (meta)data to the European Nucleotide Archive (ENA)</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.7.1</token>
+        <token name="@TOOL_VERSION@">0.7.3</token>
         <token name="@VERSION_SUFFIX@">1</token>
         <import>samples_macros.xml</import>
     </macros>
@@ -796,7 +796,7 @@
                 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/>
                 <has_text_matching expression="--action 'modify' --center 'Some research center'"/>
                 <has_text_matching expression="--checklist ERC000033"/>
-                <not_has_text text="add" />
+                <not_has_text text="--action 'add'" />
             </assert_command>
         </test>
         <!--Test 9: isa JSON input of NON-VIRAL samples-->
--- a/samples_macros.xml	Wed Mar 27 16:46:55 2024 +0000
+++ b/samples_macros.xml	Wed Jun 12 16:01:11 2024 +0000
@@ -126,13 +126,13 @@
                 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
                 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
                 <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" />
-                <param name="collection_date" type="text" label="Collection date" optional="True" help="options are: YYYY, YYYY-MM, YYYY-MM-DD, not collected, restricted access or not provided">
+                <param name="collection_date" type="text" label="Collection date" optional="False" help="options are: YYYY, YYYY-MM, YYYY-MM-DD, not collected, restricted access or not provided">
                     <option value="not collected">not collected</option>
                     <option value="restricted access">restricted access</option>
                     <option value="not provided">not provided</option>
                     <validator type="regex"  message="Data format is not valid">(^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not collected$)|(^not provided$)|(^restricted access$)</validator>
                 </param>
-                <param name="geo_location_country" type="select" label="Select the country where the sample was obtained">
+                <param name="geo_location_country" type="select" optional="False" label="Select the country where the sample was obtained">
                     <options from_data_table="geographic_location_1">
                         <column name="value" index="0"/>
                     </options>
@@ -211,13 +211,13 @@
                 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
                 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
                 <param name="tax_id" type="integer" value="0" label="Enter the taxonomic ID corresponding to the sample species" />
-                <param name="collection_date" type="text" label="Collection date" optional="True" help="options are: YYYY, YYYY-MM, YYYY-MM-DD, not collected, restricted access or not provided">
+                <param name="collection_date" type="text" label="Collection date" optional="False" help="options are: YYYY, YYYY-MM, YYYY-MM-DD, not collected, restricted access or not provided">
                     <option value="not collected">not collected</option>
                     <option value="restricted access">restricted access</option>
                     <option value="not provided">not provided</option>
                     <validator type="regex"  message="Data format is not valid">(^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not collected$)|(^not provided$)|(^restricted access$)</validator>
                 </param>
-                <param name="geo_location_country" type="select" label="Select the country where the sample was obtained">
+                <param name="geo_location_country" type="select" optional="False" label="Select the country where the sample was obtained">
                     <options from_data_table="geographic_location_1">
                         <column name="value" index="0"/>
                     </options>