annotate cfsan_snp_pipeline_merge_sites.xml @ 2:b64c03573271 draft

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<tool id="cfsan_snp_pipeline_merge_sites" name="CFSAN SNP Pipeline: merge sites" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>from multiple samples</description>
    <macros>
        <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"/>
                    <element name="input2" value="input2.vcf" ftype="vcf"/>
                    <element name="input3" value="input3.vcf" ftype="vcf"/>
                    <element name="input4" value="input4.vcf" ftype="vcf"/>
                </collection>
            </param>
            <output name="output" value="output2.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Combine the SNP positions across all samples into a single unified SNP list
file identifing the positions and sample names where SNPs were called.

**Optional parameters**

 * **force** - Force processing even when result file already exists and is newer than inputs (default: False)
 * **vcfname** - File name of the VCF files which must exist in each of the sample directories (default: var.flt.vcf)
 * **maxsnps** - Exclude samples having more than this maximum allowed number of SNPs. Set to -1 to disable this function (default: -1)

**More information**

CFSAN SNP Pipeline `merge sites documentation <https://snp-pipeline.readthedocs.io/en/latest/cmd_ref.html#merge-sites>`_
    ]]></help>
    <expand macro="citations"/>
</tool>