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34 lines
1.6 KiB
XML
34 lines
1.6 KiB
XML
<tool id="mapper2" name="mapper2" version="0.1.0">
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<command><![CDATA[
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cp '$__tool_directory__/1.bam' '$out_file1'
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]]></command>
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<inputs>
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<!-- Conditional input block loosely based on bwa-mem. -->
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<conditional name="fastq_input">
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<param name="fastq_input_selector" type="select" label="Single or Paired-end reads">
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<option value="paired">Paired</option>
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<option value="single">Single</option>
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<option value="paired_collection">Paired Collection</option>
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<option value="paired_iv">Paired Interleaved</option>
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</param>
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<when value="paired">
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<param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" />
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<param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" />
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</when>
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<when value="single">
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<param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset"/>
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</when>
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<when value="paired_collection">
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<param name="fastq_input1" type="data_collection" collection_type="paired" format="fastq" label="Select a paired collection" />
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</when>
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<when value="paired_iv">
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<param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" />
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</when>
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</conditional>
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<param name="reference" type="data" format="fasta" label="Fasta Input"/>
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</inputs>
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<outputs>
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<data name="out_file1" format="bam" />
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</outputs>
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</tool>
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