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1 <tool id="vl_tools_convert_sam" name="VLT.convert_sam">
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2 <description>converter</description>
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3 <command interpreter="bash">
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4 launcher.sh
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5 --interpreter=python
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6 --runner=convert_sam.py
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7 --logfile ${log_file} convert_sam -i ${input_file}
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8 -o ${output_file} --reftag ${dbkey} --output-format ${output_type}
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9 ## FIXME: find a way to import the default from the relevant module
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10 --flank-size 125
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11 </command>
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12 <inputs>
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13 <param name="input_file" type="data" format="sam" label="SAM input file" />
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14 <param name="output_type" type="select" label="Convert to:">
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15 <option value="marker_alignment">VL marker alignment</option>
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16 <option value="segment_extractor">Genome segment extractor</option>
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17 </param>
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18 </inputs>
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19 <outputs>
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20 <data name="output_file">
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21 <change_format>
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22 <when input="output_type" value="marker_alignment" format="tabular" />
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23 <when input="output_type" value="segment_extractor" format="interval" />
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24 </change_format>
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25 </data>
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26 <data format="txt" name="log_file" label="${tool.name}.log_file"/>
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27 </outputs>
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28 <help>
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29 **What it does**
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30
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31 This tool converts SAM alignment data to VL marker alignment or Galaxy
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32 extract genomic DNA input.
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33
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34 Expects single-end BWA alignment data produced by the previous steps
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35 in the workflow (see markers_to_fastq).
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36
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37 **NOTE:** if the marker_alignment output format is selected, the
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38 Database/Build property must be set in the input SAM file.
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39 </help>
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40 </tool>
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