comparison snippy.xml @ 1:82f2b6f20fa2 draft

planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61

0:c9a8ef2aa380

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

            #if str( $fastq_input.fastq_input_selector ) == "paired"
                --pe1 '$fastq_input.fastq_input1'
                --pe2 '$fastq_input.fastq_input2'
            #end if
            #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
                --pe1 '$fastq_input.fastq_input1.forward'
                --pe2 '$fastq_input.fastq_input1.reverse'
            #end if
            #if str( $fastq_input.fastq_input_selector ) == "single"
                --se '$fastq_input.fastq_input1'
            #end if
            #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
                --peil '$fastq_input.fastq_input1'
            #end if

        &&

        gunzip out/snps.depth.gz

        &&

        #import re
        #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
        mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&

        tar -czf out.tgz ${dir_name}


    ]]></command>

            <when value="paired">
                <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
                <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
            </when>
            <when value="single">
                <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
            </when>
            <when value="paired_collection">
                <param name="fastq_input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
            </when>
            <when value="paired_iv">
                <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
            </when>
        </conditional>

        <section name="adv" title="Advanced parameters" expanded="false">
            <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />

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

    </tests>


    <help><![CDATA[

1:82f2b6f20fa2

<tool id="snippy" name="snippy" version="@VERSION@+galaxy1">
  <description>
      Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
  </description>
  <macros>
      <import>macros.xml</import>

            #if str( $fastq_input.fastq_input_selector ) == "paired"
                --pe1 '$fastq_input.fastq_input1'
                --pe2 '$fastq_input.fastq_input2'
            #end if
            #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
                --pe1 '$fastq_input.fastq_input.forward'
                --pe2 '$fastq_input.fastq_input.reverse'
            #end if
            #if str( $fastq_input.fastq_input_selector ) == "single"
                --se '$fastq_input.fastq_input'
            #end if
            #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
                --peil '$fastq_input.fastq_input'
            #end if

        &&

        gunzip out/snps.depth.gz

        &&

        #import re
        #if str( $fastq_input.fastq_input_selector ) == "paired"
            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
        #else
            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier)
        #end if

        mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa ${dir_name}/ &&
        tar -czf out.tgz ${dir_name}


    ]]></command>

            <when value="paired">
                <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
                <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
            </when>
            <when value="single">
                <param name="fastq_input" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
            </when>
            <when value="paired_collection">
                <param name="fastq_input" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
            </when>
            <when value="paired_iv">
                <param name="fastq_input" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
            </when>
        </conditional>

        <section name="adv" title="Advanced parameters" expanded="false">
            <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />

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

        <test> <!-- test 6 - fasta ref default paired_collection -->
	    <param name="ref" value="wildtype.fna" ftype="fasta" />
            <param name="fastq_input_selector" value="paired_collection" />
            <param name="fastq_input">
                <collection type="paired">
                    <element name="forward" ftype="fastqsanger" value="mutant_R1.fastq" />
                    <element name="reverse" ftype="fastqsanger" value="mutant_R2.fastq" />
                </collection>
            </param>
            <param name="outputs" value="outgff,outsum" />
            <output name="snpsum" ftype="tabular" file="fna_ref/snps.txt" lines_diff="6" />
            <output name="snpgff" ftype="gff3" file="fna_ref/snps.gff" />
        </test>

    </tests>


    <help><![CDATA[