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bgrueningbgruening
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add view tools, as this is also needed for gfa conversion
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‎tools/vg/view.xml‎

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<tool id="vg_view" name="vg view" version="@TOOL_VERSION@">
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<description></description>
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<macros>
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<import>macros.xml</import>
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</macros>
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<expand macro="requirements"/>
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<command detect_errors="exit_code"><![CDATA[
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vg view
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$input_format.input_format_selector
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'$input_format.infile'
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$output_format
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--threads=\${GALAXY_SLOTS:-1}
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> '$output'
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]]></command>
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<inputs>
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<conditional name="input_format">
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<param name="input_format_selector" type="select" label="Your input is in format">
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<option value="--vg-in" selected="true">variant graph (vg)</option>
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<option value="--json-in">JSON</option>
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<option value="--gfa-in">GFA</option>
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<option value="--bam">BAM</option>
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</param>
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<when value="--vg-in">
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<param name="infile" type="data" format="vg" label="Input file in variant graph format (vg)" />
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</when>
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<when value="--gfa-in">
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<param name="infile" type="data" format="gfa1" label="Input file in Graphical Fragment Assembly (gfa)" />
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</when>
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<when value="--json-in">
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<param name="infile" type="data" format="json" label="Input file in JSON" />
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</when>
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<when value="--bam">
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<param name="infile" type="data" format="bam" label="Input file in BAM" />
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</when>
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</conditional>
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<param name="output_format" type="select" label="Choose your output format">
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<option value="--vg">VG</option>
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<option value="--json">JSON</option>
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<option value="--gfa">GFA</option>
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<option value="--dot">dot</option>
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</param>
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</inputs>
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<outputs>
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<data name="output" format="vg">
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<change_format>
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<when input="output_format" value="--dot" format="graph_dot"/>
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<when input="output_format" value="--json" format="json"/>
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<when input="output_format" value="--gfa" format="gfa1"/>
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</change_format>
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</data>
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</outputs>
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<tests>
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<test>
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<conditional name="input_format">
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<param name="input_format_selector" value="--gfa-in" />
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<param name="infile" value="x.gfa" ftype="gfa1" />
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</conditional>
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<param name="output_format" value="--vg" />
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<output name="output" file="x.vg" ftype="vg" />
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</test>
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<test>
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<conditional name="input_format">
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<param name="input_format_selector" value="--vg-in" />
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<param name="infile" value="x.vg" />
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</conditional>
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<param name="output_format" value="--json" />
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<output name="output" file="x.json" ftype="json" />
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</test>
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<test>
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<conditional name="input_format">
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<param name="input_format_selector" value="--json-in" />
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<param name="infile" value="x.json" ftype="json" />
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</conditional>
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<param name="output_format" value="--vg" />
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<output name="output" file="x.vg" ftype="vg" />
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</test>
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</tests>
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<help><![CDATA[
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variation graph (vg) view module
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-----------------------------------
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Inspect and convert variant graphs in different file formats.
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]]></help>
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<expand macro="citations" />
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</tool>

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