Mercurial > repos > iuc > vsnp_get_snps

comparison vsnp_get_snps.xml @ 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 9ac0b1d5560d
children 4535ad8b74f3
comparison
equal deleted inserted replaced
2:6fdfdee72f8a 3:ae7b1b97a2a0
1 <tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
46 ln -s '${i}' '$input_vcf_dir/${zc_vcf_identifier}' && 46 ln -s '${i}' '$input_vcf_dir/${zc_vcf_identifier}' &&
47 #end for 47 #end for
48 #end if 48 #end if
49 #if str($input_excel_cond.input_excel_param) == 'yes': 49 #if str($input_excel_cond.input_excel_param) == 'yes':
50 #if str($input_excel_cond.excel_source_cond.excel_source) == 'cached': 50 #if str($input_excel_cond.excel_source_cond.excel_source) == 'cached':
51 #set excel_file = 'No genome specified for input VCF (database) file(s)' 51 ## The selected Excel filter must be associated with the dbkey value defined above.
52 #set excel_fields = $__app__.tool_data_tables['vsnp_excel'].get_fields() 52 #set excel_file = $input_excel_cond.excel_source_cond.input_excel.fields.path
53 ## The value of excel_fields is a nested list that looks like this.
54 ## [['AF2122', 'Mbovis_define_filter.xlsx', '~/tool-data/vsnp/AF2122/excel/Mbovis_define_filter.xlsx', 'Excel file for AF2122'],...]
55 #for $i in $excel_fields:
56 #if str($i[0]) == $dbkey:
57 #set excel_file = $i[2]
58 #break
59 #end if
60 #end for
61 #else: 53 #else:
62 #set excel_file = $input_excel_cond.excel_source_cond.input_excel 54 #set excel_file = $input_excel_cond.excel_source_cond.input_excel
63 #end if 55 #end if
64 #end if 56 #end if
65 python '$__tool_directory__/vsnp_get_snps.py' 57 python '$__tool_directory__/vsnp_get_snps.py'
116 <param name="excel_source" type="select" label="Choose the source for the Excel file"> 108 <param name="excel_source" type="select" label="Choose the source for the Excel file">
117 <option value="cached">locally cached</option> 109 <option value="cached">locally cached</option>
118 <option value="history">from history</option> 110 <option value="history">from history</option>
119 </param> 111 </param>
120 <when value="cached"> 112 <when value="cached">
121 <param name="input_excel" type="select" label="Excel file"> 113 <param name="input_excel" type="select" label="Excel file" help="Select the file associated with the same dbkey as the input VCF file(s)">
122 <options from_data_table="vsnp_excel"> 114 <options from_data_table="vsnp_excel">
123 <validator type="no_options" message="No built-in Excel grouping and filtering datasets are available"/> 115 <validator type="no_options" message="No built-in Excel grouping and filtering datasets are available"/>
124 </options> 116 </options>
125 </param> 117 </param>
126 </when> 118 </when>