comparison snippy.xml @ 5:0aa87d97847f draft

"planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"

4:9bccc8404a3c

<tool id="snippy" name="snippy" version="@VERSION@+galaxy2">
  <description>
      Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
  </description>
  <macros>
      <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="version_command" />

    <command detect_errors="exit_code"><![CDATA[

        #if $ref.is_of_type("fasta")
            cp '$ref' 'ref.fna' &&
        #end if
        #if $ref.is_of_type("genbank")
            cp '$ref' 'ref.gbk' &&
        #end if
        snippy
            --outdir 'out'
            --cpus \${GALAXY_SLOTS:-1}
            --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
            #if $ref.is_of_type("fasta")
                --ref 'ref.fna'
            #end if
            #if $ref.is_of_type("genbank")
                --ref 'ref.gbk'
            #end if
            --mapqual $adv.mapqual
            --mincov $adv.mincov
            --minfrac $adv.minfrac
            --minqual $adv.minqual
            #if $adv.rgid

        #if "outcon" in str($outputs) and $adv.rename_cons
          && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa
        #end if


    ]]></command>

    <inputs>

        <param name="ref" type="data" format="fasta,genbank" label="Reference File (either in fasta or genbank format)" help="Fasta or Genbank file to use as the reference" />

        <conditional name="fastq_input">
            <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
                <option value="paired">Paired</option>
                <option value="single">Single</option>
                <option value="paired_collection">Paired Collection</option>

            <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option>
            <option value="outsum" selected="False">A summary of the samples and mapping</option>
            <option value="outlog" selected="False">A log file with the commands run and their outputs</option>
            <option value="outaln" selected="False">A version of the reference but with - at position with depth=0 and N for 0 to depth to --mincov (does not have variants)</option>
            <option value="outcon" selected="False">A version of the reference genome with all variants instantiated</option>
            <option value="outdep" selected="False">Output of samtools depth for the .bam file</option>
            <option value="outbam" selected="False">The alignments in BAM format. Note that multi-mapping and unmapped reads are not present.</option>
            <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option>
        </param>

    </inputs>

            <filter>outputs and 'outaln' in outputs</filter>
        </data>
        <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
            <filter>outputs and 'outcon' in outputs</filter>
        </data>
        <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth">
            <filter>outputs and 'outdep' in outputs</filter>
        </data>
        <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
            <filter>outputs and 'outbam' in outputs</filter>
        </data>
        <data format="zip" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
            <filter>outputs and 'outzip' in outputs</filter>

    </outputs>

    <tests>

        <test> <!-- test 0 - fasta ref no snps -->
            <param name="ref" value="reference.fasta" ftype="fasta" />
            <param name="fastq_input_selector" value="paired" />
            <param name="fastq_input1" ftype="fastqsanger" value="a_1.fastq" />
            <param name="fastq_input2" ftype="fastqsanger" value="a_2.fastq" />
            <param name="mincov" value="2" />
            <param name="minqual" value="60" />
            <param name="outputs" value="outgff,outsum" />
            <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
            <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" />
        </test>

        <test> <!-- test 1 - fasta ref one snp -->
            <param name="ref" value="reference.fasta" ftype="fasta" />
            <param name="fastq_input_selector" value="paired" />
            <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" />
            <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" />
            <param name="mincov" value="2" />
            <param name="minqual" value="60" />
            <param name="outputs" value="outgff,outsum" />
            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
            <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
        </test>

        <test> <!-- test 2 - fasta ref one snp paired_collection -->
            <param name="ref" value="reference.fasta" ftype="fasta" />
            <param name="fastq_input_selector" value="paired_collection" />
            <param name="fastq_input">
                <collection type="paired">
                    <element name="forward" ftype="fastqsanger" value="b_1.fastq" />
                    <element name="reverse" ftype="fastqsanger" value="b_2.fastq" />

            <param name="outputs" value="outgff,outsum" />
            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
            <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
        </test>

        <test> <!-- test 3 - fasta ref one snp single -->
            <param name="ref" value="reference.fasta" ftype="fasta" />
            <param name="fastq_input_selector" value="single" />
            <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
            <param name="mincov" value="2" />
            <param name="minqual" value="60" />
            <param name="outputs" value="outgff,outsum" />
            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
            <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
        </test>
    </tests>


    <help><![CDATA[

**Further information**

    For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy

    ]]></help>
  <expand macro="citations"/>

</tool>

5:0aa87d97847f

<tool id="snippy" name="snippy" version="@VERSION@+galaxy0">
  <description>
      Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />

    <command detect_errors="exit_code"><![CDATA[

        @REFERENCE_SOURCE_FILE@

        snippy
            --outdir 'out'
            --cpus \${GALAXY_SLOTS:-1}
            --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
            @REFERENCE_COMMAND@
            --mapqual $adv.mapqual
            --mincov $adv.mincov
            --minfrac $adv.minfrac
            --minqual $adv.minqual
            #if $adv.rgid

        #if "outcon" in str($outputs) and $adv.rename_cons
          && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa
        #end if


    ]]>    </command>

    <inputs>
        <expand macro="reference_selector" />
        <conditional name="fastq_input">
            <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
                <option value="paired">Paired</option>
                <option value="single">Single</option>
                <option value="paired_collection">Paired Collection</option>

            <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option>
            <option value="outsum" selected="False">A summary of the samples and mapping</option>
            <option value="outlog" selected="False">A log file with the commands run and their outputs</option>
            <option value="outaln" selected="False">A version of the reference but with - at position with depth=0 and N for 0 to depth to --mincov (does not have variants)</option>
            <option value="outcon" selected="False">A version of the reference genome with all variants instantiated</option>
            <option value="outbam" selected="False">The alignments in BAM format. Note that multi-mapping and unmapped reads are not present.</option>
            <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option>
        </param>

    </inputs>

            <filter>outputs and 'outaln' in outputs</filter>
        </data>
        <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
            <filter>outputs and 'outcon' in outputs</filter>
        </data>
        <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
            <filter>outputs and 'outbam' in outputs</filter>
        </data>
        <data format="zip" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
            <filter>outputs and 'outzip' in outputs</filter>

    </outputs>

    <tests>

        <test>            <!-- test 0 - fasta ref no snps -->
            <!-- <param name="ref" value="reference.fasta" ftype="fasta" /> -->
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" value="reference.fasta" ftype="fasta"/>
            </conditional>
            <param name="fastq_input_selector" value="paired" />
            <param name="fastq_input1" ftype="fastqsanger" value="a_1.fastq" />
            <param name="fastq_input2" ftype="fastqsanger" value="a_2.fastq" />
            <param name="mincov" value="2" />
            <param name="minqual" value="60" />
            <param name="outputs" value="outgff,outsum" />
            <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
            <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" />
        </test>

        <test>            <!-- test 1 - fasta ref one snp -->
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" value="reference.fasta" ftype="fasta"/>
            </conditional>
            <param name="fastq_input_selector" value="paired" />
            <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" />
            <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" />
            <param name="mincov" value="2" />
            <param name="minqual" value="60" />
            <param name="outputs" value="outgff,outsum" />
            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
            <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
        </test>

        <test>            <!-- test 2 - fasta ref one snp paired_collection -->
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" value="reference.fasta" ftype="fasta"/>
            </conditional>
            <param name="fastq_input_selector" value="paired_collection" />
            <param name="fastq_input">
                <collection type="paired">
                    <element name="forward" ftype="fastqsanger" value="b_1.fastq" />
                    <element name="reverse" ftype="fastqsanger" value="b_2.fastq" />

            <param name="outputs" value="outgff,outsum" />
            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
            <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
        </test>

        <test>            <!-- test 3 - fasta ref one snp single -->
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" value="reference.fasta" ftype="fasta"/>
            </conditional>
            <param name="fastq_input_selector" value="single" />
            <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
            <param name="mincov" value="2" />
            <param name="minqual" value="60" />
            <param name="outputs" value="outgff,outsum" />
            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
            <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
        </test>

        <test>            <!-- test 4 - reference source as cached -->
            <conditional name="reference_source">
                <param name="reference_source_selector" value="cached"/>
                <param name="ref_file" value="test_id"/>
            </conditional>
            <param name="fastq_input_selector" value="single" />
            <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
            <param name="mincov" value="2" />
            <param name="minqual" value="60" />
            <param name="outputs" value="outgff,outsum" />
            <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
            <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
        </test>
    </tests>


    <help><![CDATA[

**Further information**

    For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy

    ]]>    </help>
    <expand macro="citations"/>

</tool>