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changeset 1:997f15134095 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
author iuc
date Mon, 19 Aug 2024 10:50:07 +0000
parents 25424cc216f9
children 398000f8de7d
files cnv.xml macros.xml
diffstat 2 files changed, 36 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/cnv.xml	Mon Jul 22 12:36:12 2024 +0000
+++ b/cnv.xml	Mon Aug 19 10:50:07 2024 +0000
@@ -31,15 +31,24 @@
         #if str($advanced_settings.chromosome)
             --chromosome '$advanced_settings.chromosome'
         #end if
-        #if str($advanced_settings.variantStateId)
+        #if str($advanced_settings.variantStateId) and $advanced_settings.variantStateId != ""
             --variantStateId '$advanced_settings.variantStateId'
         #end if
-        #if str($advanced_settings.variantState)
-            --variantState '$advanced_settings.variantState'
-        #end if
         #if str($advanced_settings.sequenceId)
             --sequenceId '$advanced_settings.sequenceId'
         #end if
+        #if str($advanced_settings.variantType)
+            --variantType '$advanced_settings.variantType'
+        #end if
+        #if str($advanced_settings.primarySite)
+            --primarySite '$advanced_settings.primarySite'
+        #end if
+        #if str($advanced_settings.diseaseType)
+            --diseaseType '$advanced_settings.diseaseType'
+        #end if
+        #if str($advanced_settings.gene)
+            --gene '$advanced_settings.gene'
+        #end if
         > cnv_query_findings.json
     ]]></command>
     <expand macro="configfile"/>
@@ -53,9 +62,22 @@
             <param argument="--start" optional="true" type="integer" label="START" value="" help="Start position" />
             <param argument="--end" optional="true" type="integer" label="END" value="" help="End position" />
             <param argument="--chromosome" optional="true" type="text" label="CHROMOSOME" value="" help="Chromosome numbers (without chr)" />
-            <param argument="--variantStateId" optional="true" type="text" label="VARIANT STATE ID" value="" help="E.g EFO:0030067" />
-            <param argument="--variantState" optional="true" type="text" label="VARIANT STATE" value="" help="E.g. copy number loss" />
+            <param argument="variantStateId" optional="true" type="select" label="GENDERS" help="">
+            <option value="EFO:0030070">EFO:0030070: copy number gain</option>
+            <option value="EFO:0030071">EFO:0030071: low-level copy number gain</option>
+            <option value="EFO:0030072">EFO:0030072: high-level copy number gain</option>
+            <option value="EFO:0030073">EFO:0030073: focal genome amplification</option>
+            <option value="EFO:0030067">EFO:0030067: copy number loss</option>
+            <option value="EFO:0030068">EFO:0030068: low-level copy number loss</option>
+            <option value="EFO:0020073">EFO:0020073: high-level copy number loss</option>
+            <option value="EFO:0030069">EFO:0030069: complete genomic deletion</option>
+            <option value="" selected="True">non specific</option>
+            </param>
             <param argument="--sequenceId" optional="true" type="text" label="SEQUENCE ID" value="" help="E.g. refseq:NC_000011.10" />
+            <param argument="--gene" optional="true" type="text" label="GENE NAME" value="" help="Gene name e.g. 'AL645728.1'" />
+            <param argument="--variantType" optional="true" type="text" label="VARIANT TYPE" value="" help="Variant Type 'DEL' or 'DUP'" />
+            <param argument="--primarySite" optional="true" type="text" label="PRIMARY SITE" value="" help="Primary Site, e.g. 'brain'" />
+            <param argument="--diseaseType" optional="true" type="text" label="DISEASE TYPE" value="" help="Disease Type, e.g. 'adnexal and skin appendage neoplasms'" />
         </section>
     </inputs>
     <outputs>
@@ -64,11 +86,14 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="database" value="beacon" />
-            <param name="collection" value="cnv" />
+            <param name="collection" value="test" />
             <param name="db_host" value="20.108.51.167" />
-            <param name="chromosome" value="1" />
-            <param name="start" value="243618689" />
-            <param name="end" value="243620819" />
+            <param name="chromosome" value="17" />
+            <param name="start" value="43044295" />
+            <param name="end" value="43170245" />
+            <param name="primarySite" value="breast" />
+            <param name="diseaseType" value="adnexal and skin appendage neoplasms" />
+            <param name="gene" value="BRCA1" />
             <param name="variantStateId" value="EFO:0030068" />
             <output name="out_cnv_query">
                 <assert_contents><has_text_matching expression="_id"/></assert_contents>
--- a/macros.xml	Mon Jul 22 12:36:12 2024 +0000
+++ b/macros.xml	Mon Aug 19 10:50:07 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@TOOL_VERSION@">2.2.1</token>
+    <token name="@TOOL_VERSION@">2.2.3</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">beacon2-import</requirement>