comparison cfsan_snp_pipeline_merge_sites.xml @ 3:bb483baa0e50 draft

Uploaded

2:b64c03573271

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/snp_wind.py' ./
#if str($input_type_cond.input_type) == 'single':
    -n '$input_type_cond.input_vcf.element_identifier'
    -f '$input_type_cond.input_vcf'
#else:
    #for $input_vcf in $input_type_cond.input_vcf_collection:
        -n '$input_vcf.element_identifier'
        -f '$input_vcf'
    #end for
#end if
-p 'var.fit.vcf' > ./file
&& cfsan_snp_pipeline merge_sites -v 4 -n 'var.fit.vcf' ./file ./filtered_snps -o '$output'
    ]]></command>
    <inputs>
        <expand macro="input_type_cond"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input_vcf" value="input1.vcf"/>
            <output name="output" value="output.tabular"/>
        </test>
        <test>
            <param name="input_type" value="collection"/>
            <param name="input_vcf_collection">
                <collection type="list">
                    <element name="input1" value="input1.vcf" ftype="vcf"/>

3:bb483baa0e50

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/snp_wind.py' ./
#for $input_vcf in $input_vcf_collection:
    -n '$input_vcf.element_identifier' -f '$input_vcf'
#end for
-p 'var.fit.vcf' > ./file
&& cfsan_snp_pipeline merge_sites -v 4 -n 'var.fit.vcf' ./file ./filtered_snps -o '$output'
    ]]></command>
    <inputs>
        <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input_type" value="collection"/>
            <param name="input_vcf_collection">
                <collection type="list">
                    <element name="input1" value="input1.vcf" ftype="vcf"/>