comparison bwa.xml @ 13:53646aaaafef draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 3442b18860bc4398d917e3a35943351a9cf031ea

12:bd3a1e0de84c

        <option value="single">Single fastq</option>
        <option value="paired_bam">Paired BAM</option>
        <option value="single_bam">Single BAM</option>
      </param>
      <when value="paired">
        <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
        <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
        <conditional name="adv_pe_options">

          <expand macro="advanced_pe_options" />

        </conditional>
      </when>

      <when value="paired_collection">
        <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
        <conditional name="adv_pe_options">

          <expand macro="advanced_pe_options" />

        </conditional>
      </when>

      <when value="single">
        <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
        <conditional name="adv_se_options">

          <expand macro="advanced_se_options" />

        </conditional>

    <test>
      <param name="reference_source_selector" value="history" />
      <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
      <param name="input_type_selector" value="paired"/>
      <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
      <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
      <param name="analysis_type_selector" value="illumina"/>
      <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2" />
    </test>
    <test>

13:53646aaaafef

        <option value="single">Single fastq</option>
        <option value="paired_bam">Paired BAM</option>
        <option value="single_bam">Single BAM</option>
      </param>
      <when value="paired">
        <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
        <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
        <conditional name="adv_pe_options">

          <expand macro="advanced_pe_options" />

        </conditional>
      </when>

      <when value="paired_collection">
        <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
        <conditional name="adv_pe_options">

          <expand macro="advanced_pe_options" />

        </conditional>
      </when>

      <when value="single">
        <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
        <conditional name="adv_se_options">

          <expand macro="advanced_se_options" />

        </conditional>

    <test>
      <param name="reference_source_selector" value="history" />
      <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
      <param name="input_type_selector" value="paired"/>
      <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
      <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
      <param name="analysis_type_selector" value="illumina"/>
      <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2" />
    </test>
    <test>
      <param name="reference_source_selector" value="history" />
      <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
      <param name="input_type_selector" value="paired"/>
      <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
      <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
      <param name="analysis_type_selector" value="illumina"/>
      <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2" />
    </test>
    <test>