# HG changeset patch
# User nml
# Date 1623445697 0
# Node ID d1085589a5a78e3dc313262321f398c33afca2de
# Parent  65521c432f58fe95acd5777a4a2c4fc976ec1777
"planemo upload for repository https://github.com/phac-nml/gnali/ commit 8779aba2c77e9ed7364c91e04a75b9c3468b7143"

diff -r 65521c432f58 -r d1085589a5a7 gnali.xml
--- a/gnali.xml	Tue May 04 15:13:43 2021 +0000
+++ b/gnali.xml	Fri Jun 11 21:08:17 2021 +0000
@@ -1,5 +1,5 @@
-<tool id="gnali" name="gNALI" version="@VERSION@" python_template_version="3.7">
-    <description>Get nonessential, LoF variants</description>
+<tool id="gnali" name="gNALI" version="@VERSION@" python_template_version="3.7" profile="@PROFILE_VERSION@">
+    <description>Get and filter nonessential, loss-of-function variants</description>
     <macros>
         <import>macros.xml</import>
     </macros>  
@@ -29,16 +29,16 @@
         <conditional name="database_info">
             <param type="select" name="database" label="Database" format="txt" help="Database to query" >
                 <option value="gnomadv2.1.1" selected="true">gnomADv2.1.1 (GRCh37/hg19)</option>
-                <option value="gnomadv3">gnomADv3 (GRCh38/hg38)</option>
+                <option value="gnomadv3.1.1">gnomADv3.1.1 (GRCh38/hg38)</option>
             </param>
             <when value="gnomadv2.1.1">
                 <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters">
                     <option value="homozygous-controls">homozygous controls (controls_nhomalt>0)</option>
                     <option value="heterozygous-controls">heterozygous controls (controls_nhomalt=0)</option>
-                    <option value="nhomalt>0">homozygous (nhomalt>0)</option>
+                    <option value="homozygous">homozygous (nhomalt>0)</option>
                 </param>
             </when>
-            <when value="gnomadv3">
+            <when value="gnomadv3.1.1">
                 <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters">
                     <option value="homozygous">homozygous (nhomalt>0)</option>
                     <option value="heterozygous">heterozygous (nhomalt=0)</option>
@@ -96,7 +96,7 @@
 potential loss of function variants of genes.
 
 NOTE: loss-of-function is influenced by the genome build. Not all variants available in gnomADv2.1.1 are
-available in gnomADv3 and vice versa.
+available in gnomADv3.1.1 and vice versa.
 
 Usage
 -----------
diff -r 65521c432f58 -r d1085589a5a7 macros.xml
--- a/macros.xml	Tue May 04 15:13:43 2021 +0000
+++ b/macros.xml	Fri Jun 11 21:08:17 2021 +0000
@@ -1,5 +1,6 @@
 <macros>
-    <token name="@VERSION@">1.0.4</token>
+    <token name="@VERSION@">1.0.5</token>
+    <token name="@PROFILE_VERSION@">20.01</token>
     <xml name="requirements">
     <requirements>
     <requirement type="package" version ="@VERSION@">gnali</requirement>
diff -r 65521c432f58 -r d1085589a5a7 test-data/results/Nonessential_Host_Genes_Basic.txt
--- a/test-data/results/Nonessential_Host_Genes_Basic.txt	Tue May 04 15:13:43 2021 +0000
+++ b/test-data/results/Nonessential_Host_Genes_Basic.txt	Fri Jun 11 21:08:17 2021 +0000
@@ -1,2 +1,3 @@
-HGNC_Symbol
-CCR5
+HGNC_Symbol	Status
+CCR5	HC LoF found
+ALCAM	HC LoF found, failed filtering
diff -r 65521c432f58 -r d1085589a5a7 test-data/test_genes.txt
--- a/test-data/test_genes.txt	Tue May 04 15:13:43 2021 +0000
+++ b/test-data/test_genes.txt	Fri Jun 11 21:08:17 2021 +0000
@@ -1,2 +1,2 @@
 CCR5
-ALCAM
+ALCAM
\ No newline at end of file