Mercurial > repos > greg > vsnp_get_snps

comparison vsnp_get_snps.xml @ 7:2286f3a13e4d draft

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author greg
date Thu, 22 Jul 2021 18:02:12 +0000
parents 49aceeefab0a
children 5e4595b9f63c
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6:49aceeefab0a 7:2286f3a13e4d
1 <tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@WRAPPER_VERSION@.1" profile="@PROFILE@"> 1 <tool id="vsnp_get_snps" name="vSNP: get SNPs" version="@WRAPPER_VERSION@.0+galaxy0" 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>
7 <requirement type="package" version="0.25.3">pandas</requirement> 7 <requirement type="package" version="3.0.7">openpyxl</requirement>
8 <requirement type="package" version="1.3.0">pandas</requirement>
8 <requirement type="package" version="0.6.8">pyvcf</requirement> 9 <requirement type="package" version="0.6.8">pyvcf</requirement>
9 <requirement type="package" version="1.2.0">xlrd</requirement> 10 <requirement type="package" version="2.0.1">xlrd</requirement>
10 </requirements> 11 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
12 #import re 13 #import re
13 14
14 #set input_vcf_dir = 'input_vcf_dir' 15 #set input_vcf_dir = 'input_vcf_dir'
107 <option value="history">from history</option> 108 <option value="history">from history</option>
108 </param> 109 </param>
109 <when value="cached"> 110 <when value="cached">
110 <param name="input_excel" type="select" label="Excel file"> 111 <param name="input_excel" type="select" label="Excel file">
111 <options from_data_table="vsnp_excel"> 112 <options from_data_table="vsnp_excel">
113 <filter type="data_meta" column="0" key="dbkey" ref="input_vcf_collection"/>
112 <validator type="no_options" message="No built-in Excel grouping and filtering datasets are available"/> 114 <validator type="no_options" message="No built-in Excel grouping and filtering datasets are available"/>
113 </options> 115 </options>
114 </param> 116 </param>
115 </when> 117 </when>
116 <when value="history"> 118 <when value="history">
182 <param name="input_excel_param" value="no"/> 184 <param name="input_excel_param" value="no"/>
183 <output_collection name="snps" type="list" count="1"> 185 <output_collection name="snps" type="list" count="1">
184 <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/> 186 <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/>
185 </output_collection> 187 </output_collection>
186 <output_collection name="json_avg_mq" type="list" count="1"> 188 <output_collection name="json_avg_mq" type="list" count="1">
187 <element name="all_vcf" file="json_avg_mq_all_vcf2.json" ftype="json" compare="contains"/> 189 <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/>
188 </output_collection> 190 </output_collection>
189 <output_collection name="json_snps" type="list" count="1"> 191 <output_collection name="json_snps" type="list" count="1">
190 <element name="all_vcf" file="json_all_vcf2.json" ftype="json" compare="contains"/> 192 <element name="all_vcf" file="json_all_vcf.json" ftype="json" compare="contains"/>
191 </output_collection> 193 </output_collection>
192 <output name="output_summary" file="output_summary2.html" ftype="html" compare="contains"/> 194 <output name="output_summary" file="output_summary2.html" ftype="html" compare="contains"/>
193 </test> 195 </test>
194 <!-- An input collection, an excel file, all_isolates is False --> 196 <!-- An input collection, an excel file, all_isolates is False -->
195 <test expect_num_outputs="4"> 197 <test expect_num_outputs="4">
239 <param name="input_excel_param" value="yes"/> 241 <param name="input_excel_param" value="yes"/>
240 <param name="input_excel" value="89"/> 242 <param name="input_excel" value="89"/>
241 <param name="all_isolates" value="--all_isolates"/> 243 <param name="all_isolates" value="--all_isolates"/>
242 <output_collection name="snps" type="list" count="2"> 244 <output_collection name="snps" type="list" count="2">
243 <element name="Mbovis-17" file="Mbovis-17_snps.fasta" ftype="fasta"/> 245 <element name="Mbovis-17" file="Mbovis-17_snps.fasta" ftype="fasta"/>
244 <element name="all_vcf" file="all_vcf3.fasta" ftype="fasta"/> 246 <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/>
245 </output_collection> 247 </output_collection>
246 <output_collection name="json_avg_mq" type="list" count="2"> 248 <output_collection name="json_avg_mq" type="list" count="2">
247 <element name="Mbovis-17" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/> 249 <element name="Mbovis-17" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/>
248 <element name="all_vcf" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/> 250 <element name="all_vcf" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/>
249 </output_collection> 251 </output_collection>