Mercurial > repos > iuc > vsnp_get_snps

changeset 3:ae7b1b97a2a0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 9e9e1db5b9ca53d690ed795aab1e7437f0a1c864"
author iuc
date Sat, 09 Apr 2022 09:01:11 +0000
parents 6fdfdee72f8a
children 4535ad8b74f3
files vsnp_get_snps.xml
diffstat 1 files changed, 4 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/vsnp_get_snps.xml	Mon Dec 06 18:28:42 2021 +0000
+++ b/vsnp_get_snps.xml	Sat Apr 09 09:01:11 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -48,16 +48,8 @@
 #end if
 #if str($input_excel_cond.input_excel_param) == 'yes':
     #if str($input_excel_cond.excel_source_cond.excel_source) == 'cached':
-        #set excel_file = 'No genome specified for input VCF (database) file(s)'
-        #set excel_fields = $__app__.tool_data_tables['vsnp_excel'].get_fields()
-        ## The value of excel_fields is a nested list that looks like this.
-        ## [['AF2122', 'Mbovis_define_filter.xlsx', '~/tool-data/vsnp/AF2122/excel/Mbovis_define_filter.xlsx', 'Excel file for AF2122'],...]
-        #for $i in $excel_fields:
-            #if str($i[0]) == $dbkey:
-                #set excel_file = $i[2]
-                #break
-            #end if
-        #end for
+        ## The selected Excel filter must be associated with the dbkey value defined above.
+        #set excel_file = $input_excel_cond.excel_source_cond.input_excel.fields.path
     #else:
         #set excel_file = $input_excel_cond.excel_source_cond.input_excel
     #end if
@@ -118,7 +110,7 @@
                         <option value="history">from history</option>
                     </param>
                     <when value="cached">
-                        <param name="input_excel" type="select" label="Excel file">
+                        <param name="input_excel" type="select" label="Excel file" help="Select the file associated with the same dbkey as the input VCF file(s)">
                             <options from_data_table="vsnp_excel">
                                 <validator type="no_options" message="No built-in Excel grouping and filtering datasets are available"/>
                             </options>