comparison vsnp_get_snps.xml @ 1:770834ba75e4 draft

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0:ee4ef1fc23c6

#set reference = '?'
#for $i in $input_vcf_collection:
    #set reference = $i.metadata.dbkey
    #set filename = $i.file_name
    #set name = $i.name
    ln -s $filename $input_vcf_dir/$name &&
#end for
#if str($input_zc_vcf_type) == "single":
    #set input_zc_vcf = $input_zc_vcf_type_cond.input_zc_vcf
    #set file_name_base = $os.path.basename($input_zc_vcf.file_name)
    ln -s $input_zc_vcf $input_vcf_dir/$file_name_base &&
#else
    #for $i in $input_zc_vcf_type_cond.input_zc_vcf_collection:
        #set filename = $i.file_name
        #set name = $i.name
        ln -s $filename $input_vcf_dir/$name &&
    #end for
#end if
#if str($excel_grouper_cond.excel_grouper) == "yes":
    #set excel_grouper_source = $excel_grouper_cond.excel_grouper_source_cond.excel_grouper_source
    #if str($excel_grouper_source) == "cached":
        #set excel_fields = $__app__.tool_data_tables['vsnp_excel'].get_fields()
        #for $i in $excel_fields:
            #if str($i[0]) == $reference:

    #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 ${on_string}">
            <discover_datasets pattern="__name__" directory="output_snps_dir" format="fasta" />
        </collection>
        <collection name="json_avg_mq" type="list" label="${tool.name} (average MQ) on ${on_string}">
            <discover_datasets pattern="__name__" directory="output_json_avg_mq_dir" format="json" />
        </collection>
        <collection name="json_snps" type="list" label="${tool.name} (SNPs as json) on ${on_string}">
            <discover_datasets pattern="__name__" directory="output_json_snps_dir" format="json" />
        </collection>
        <data name="output_summary" format="html" label="${tool.name} (summary) on ${on_string}"/>
    </outputs>
    <tests>
        <test>

**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},

1:770834ba75e4

#set reference = '?'
#for $i in $input_vcf_collection:
    #set reference = $i.metadata.dbkey
    #set filename = $i.file_name
    #set name = $i.name
    ln -s '$filename' '$input_vcf_dir/$name' &&
#end for
#if str($input_zc_vcf_type) == "single":
    #set input_zc_vcf = $input_zc_vcf_type_cond.input_zc_vcf
    #set file_name_base = $os.path.basename($input_zc_vcf.file_name)
    ln -s '$input_zc_vcf' '$input_vcf_dir/$file_name_base' &&
#else
    #for $i in $input_zc_vcf_type_cond.input_zc_vcf_collection:
        #set filename = $i.file_name
        #set name = $i.name
        ln -s '$filename' '$input_vcf_dir/$name' &&
    #end for
#end if
#if str($excel_grouper_cond.excel_grouper) == "yes":
    #set excel_file = 'No genome specified for input VCF (database) file(s)'
    #set excel_grouper_source = $excel_grouper_cond.excel_grouper_source_cond.excel_grouper_source
    #if str($excel_grouper_source) == "cached":
        #set excel_fields = $__app__.tool_data_tables['vsnp_excel'].get_fields()
        #for $i in $excel_fields:
            #if str($i[0]) == $reference:

    #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 ${on_string}">
            <discover_datasets pattern="__name__" directory="output_snps_dir" format="fasta"/>
        </collection>
        <collection name="json_avg_mq" type="list" label="${tool.name} (average MQ) on ${on_string}">
            <discover_datasets pattern="__name__" directory="output_json_avg_mq_dir" format="json"/>
        </collection>
        <collection name="json_snps" type="list" label="${tool.name} (SNPs as json) on ${on_string}">
            <discover_datasets pattern="__name__" directory="output_json_snps_dir" format="json"/>
        </collection>
        <data name="output_summary" format="html" label="${tool.name} (summary) on ${on_string}"/>
    </outputs>
    <tests>
        <test>

**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},