comparison vsnp_get_snps.xml @ 2:7471707d3fb4 draft

Uploaded

1:770834ba75e4

    #else:
        #set excel_file = $excel_grouper_cond.excel_grouper_source_cond.excel_grouper_file
    #end if
#end if
python '$__tool_directory__/vsnp_get_snps.py'
--processes \${GALAXY_SLOTS:-4}
--reference '$reference'
#if str($excel_grouper_cond.excel_grouper) == "yes":
    --excel_grouper_file '$excel_file'
#end if
#if str($all_isolates) == "Yes":

        </conditional>
        <param name="all_isolates" type="select" display="radio" label="Create table with all isolates?">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>
    </inputs>
    <outputs>
        <collection name="snps" type="list" label="${tool.name} (SNPs) on ${on_string}">
            <discover_datasets pattern="__name__" directory="output_snps_dir" format="fasta"/>
        </collection>

**Additional Options**

 * **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.
 * **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.
</help>
    <citations>
        <citation type="bibtex">
            @misc{None,
            journal = {None},

2:7471707d3fb4

    #else:
        #set excel_file = $excel_grouper_cond.excel_grouper_source_cond.excel_grouper_file
    #end if
#end if
python '$__tool_directory__/vsnp_get_snps.py'
--processes $processes
--reference '$reference'
#if str($excel_grouper_cond.excel_grouper) == "yes":
    --excel_grouper_file '$excel_file'
#end if
#if str($all_isolates) == "Yes":

        </conditional>
        <param name="all_isolates" type="select" display="radio" label="Create table with all isolates?">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>
        <param name="processes" type="integer" min="1" max="20" value="8" label="Number of processes for job splitting"/>
    </inputs>
    <outputs>
        <collection name="snps" type="list" label="${tool.name} (SNPs) on ${on_string}">
            <discover_datasets pattern="__name__" directory="output_snps_dir" format="fasta"/>
        </collection>

**Additional Options**

 * **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.
 * **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.
 * **Number of processes for job splitting** - Select the number of processes for splitting the job to shorten execution time.
</help>
    <citations>
        <citation type="bibtex">
            @misc{None,
            journal = {None},