Mercurial > repos > nml > gnali

diff gnali.xml @ 6:d1085589a5a7 draft

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"planemo upload for repository https://github.com/phac-nml/gnali/ commit 8779aba2c77e9ed7364c91e04a75b9c3468b7143"
author nml
date Fri, 11 Jun 2021 21:08:17 +0000
parents 65521c432f58
children 2b1154ae7e21
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--- 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
 -----------