Mercurial > repos > greg > vsnp_get_snps

comparison vsnp_get_snps.xml @ 2:7471707d3fb4 draft

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author greg
date Sat, 14 Nov 2020 09:16:04 +0000
parents 770834ba75e4
children 14285a94fb13
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1:770834ba75e4 2:7471707d3fb4
48 #else: 48 #else:
49 #set excel_file = $excel_grouper_cond.excel_grouper_source_cond.excel_grouper_file 49 #set excel_file = $excel_grouper_cond.excel_grouper_source_cond.excel_grouper_file
50 #end if 50 #end if
51 #end if 51 #end if
52 python '$__tool_directory__/vsnp_get_snps.py' 52 python '$__tool_directory__/vsnp_get_snps.py'
53 --processes \${GALAXY_SLOTS:-4} 53 --processes $processes
54 --reference '$reference' 54 --reference '$reference'
55 #if str($excel_grouper_cond.excel_grouper) == "yes": 55 #if str($excel_grouper_cond.excel_grouper) == "yes":
56 --excel_grouper_file '$excel_file' 56 --excel_grouper_file '$excel_file'
57 #end if 57 #end if
58 #if str($all_isolates) == "Yes": 58 #if str($all_isolates) == "Yes":
108 </conditional> 108 </conditional>
109 <param name="all_isolates" type="select" display="radio" label="Create table with all isolates?"> 109 <param name="all_isolates" type="select" display="radio" label="Create table with all isolates?">
110 <option value="No" selected="true">No</option> 110 <option value="No" selected="true">No</option>
111 <option value="Yes">Yes</option> 111 <option value="Yes">Yes</option>
112 </param> 112 </param>
113 <param name="processes" type="integer" min="1" max="20" value="8" label="Number of processes for job splitting"/>
113 </inputs> 114 </inputs>
114 <outputs> 115 <outputs>
115 <collection name="snps" type="list" label="${tool.name} (SNPs) on ${on_string}"> 116 <collection name="snps" type="list" label="${tool.name} (SNPs) on ${on_string}">
116 <discover_datasets pattern="__name__" directory="output_snps_dir" format="fasta"/> 117 <discover_datasets pattern="__name__" directory="output_snps_dir" format="fasta"/>
117 </collection> 118 </collection>
161 162
162 **Additional Options** 163 **Additional Options**
163 164
164 * **Use Excel file for grouping and filtering?** - select Yes to filter desired SNP positions by group. A cached Excel spreadsheet provides the most widely used SNP positions for grouping, but a custom spreadhseet can be selected from the current history. 165 * **Use Excel file for grouping and filtering?** - select Yes to filter desired SNP positions by group. A cached Excel spreadsheet provides the most widely used SNP positions for grouping, but a custom spreadhseet can be selected from the current history.
165 * **Job Resource Parameters** - an administrator for the Galaxy instance must configure this tool to display this option, so it may not be available. If it is, you can choose the number of processors to use for tool execution. 166 * **Job Resource Parameters** - an administrator for the Galaxy instance must configure this tool to display this option, so it may not be available. If it is, you can choose the number of processors to use for tool execution.
167 * **Number of processes for job splitting** - Select the number of processes for splitting the job to shorten execution time.
166 </help> 168 </help>
167 <citations> 169 <citations>
168 <citation type="bibtex"> 170 <citation type="bibtex">
169 @misc{None, 171 @misc{None,
170 journal = {None}, 172 journal = {None},