comparison vsnp_add_zero_coverage.xml @ 9:40b97055bb99 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3

8:18b59c38017e

    </macros>
    <requirements>
        <expand macro="biopython_requirement"/>
        <expand macro="openpyxl_requirement"/>
        <expand macro="pandas_requirement"/>
        <requirement type="package" version="0.16.0.1">pysam</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#import re

## The identifer for both of the following files is likely the same

ln -s '${bam_input}' '${bam_identifier}' &&
#set vcf_identifier = re.sub('[^\s\w\-]', '_', str($vcf_input.element_identifier)) + '.vcf'
ln -s '${vcf_input}' '${vcf_identifier}' &&

python '$__tool_directory__/vsnp_add_zero_coverage.py'
--bam_input '$bam_identifier'
--vcf_input '$vcf_identifier'
#if str($reference_cond.reference_source) == 'cached'
    --reference '$reference_cond.reference.fields.path'
#else:

            <param name="reference_source" value="history"/>
            <param name="reference" value="NC_002945v4.fasta" ftype="fasta"/>
            <output name="output_vcf" ftype="vcf">
                <assert_contents>
                    <has_size value="259726"/>
                </assert_contents>
            </output>
            <output name="output_metrics" ftype="tabular">
                <assert_contents>
                    <has_size value="109"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/>
            <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
            <param name="reference_source" value="cached"/>
            <output name="output_vcf" ftype="vcf">
                <assert_contents>
                    <has_size value="259726"/>
                </assert_contents>
            </output>
            <output name="output_metrics" ftype="tabular">
                <assert_contents>
                    <has_size value="109"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

Accepts a combination of single BAM and associated VCF files (or associated collections of each) to produce a VCF file for each
combination whose positions with no coverage are represented as "N".  These outputs are restricted to SNPs and those regions
along the reference with no coverage.

A metrics file is produced for each combination which provides the number of good SNPs, the average coverage and the genome
coverage percentage.

**Required Options**

 * **Choose the source for the reference genome** - select "locally cached" if the reference associated with the BAM and VCF files is available within the Galaxy environment or "from history" to select the reference from the current history.
    </help>

9:40b97055bb99

    </macros>
    <requirements>
        <expand macro="biopython_requirement"/>
        <expand macro="openpyxl_requirement"/>
        <expand macro="pandas_requirement"/>
        <requirement type="package" version="0.19.1">pysam</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#import re

## The identifer for both of the following files is likely the same

ln -s '${bam_input}' '${bam_identifier}' &&
#set vcf_identifier = re.sub('[^\s\w\-]', '_', str($vcf_input.element_identifier)) + '.vcf'
ln -s '${vcf_input}' '${vcf_identifier}' &&

python '$__tool_directory__/vsnp_add_zero_coverage.py'
--dbkey '$bam_input.metadata.dbkey'
--bam_input '$bam_identifier'
--vcf_input '$vcf_identifier'
#if str($reference_cond.reference_source) == 'cached'
    --reference '$reference_cond.reference.fields.path'
#else:

            <param name="reference_source" value="history"/>
            <param name="reference" value="NC_002945v4.fasta" ftype="fasta"/>
            <output name="output_vcf" ftype="vcf">
                <assert_contents>
                    <has_size value="259726"/>
                    <has_text text="##fileformat=VCFv4.2"/>
                </assert_contents>
            </output>
            <output name="output_metrics" ftype="tabular">
                <assert_contents>
                    <has_size value="190"/>
                    <has_text text="# BAM File"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/>
            <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
            <param name="reference_source" value="cached"/>
            <output name="output_vcf" ftype="vcf">
                <assert_contents>
                    <has_size value="259726"/>
                    <has_text text="##fileformat=VCFv4.2"/>
                </assert_contents>
            </output>
            <output name="output_metrics" ftype="tabular">
                <assert_contents>
                    <has_size value="190"/>
                    <has_text text="# BAM File"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

Accepts a combination of single BAM and associated VCF files (or associated collections of each) to produce a VCF file for each
combination whose positions with no coverage are represented as "N".  These outputs are restricted to SNPs and those regions
along the reference with no coverage.

A metrics file is produced for each combination which provides the reference length, genome coverage, average coverage, 
total zero coverage, zero coverage percent and quality SNPs.

**Required Options**

 * **Choose the source for the reference genome** - select "locally cached" if the reference associated with the BAM and VCF files is available within the Galaxy environment or "from history" to select the reference from the current history.
    </help>