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25 lines
1.6 KiB
XML
25 lines
1.6 KiB
XML
<tool id="gmaj_1" name="GMAJ">
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<description>Multiple Alignment Viewer</description>
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<command interpreter="python2.4">GMAJ.py $out_file1 $maf_input $dbkey $exons_file $highlights_file $underlays_file $repeats_file $links_file</command>
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<inputs>
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<param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/>
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<param name="exons_file" type="data" format="bed" label="Exons File" optional="True"/>
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<param name="highlights_file" type="data" format="bed" label="Highlights File" optional="True"/>
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<param name="underlays_file" type="data" format="bed" label="Underlays File" optional="True"/>
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<param name="repeats_file" type="data" format="bed" label="Repeats File" optional="True"/>
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<param name="links_file" type="data" format="bed" label="Links File" optional="True"/>
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</inputs>
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<outputs>
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<data name="out_file1" format="gmaj.zip"/>
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</outputs>
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<help>
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You can use this tool to view a set of MAF alignments. You may also include optional additional information about the primary organism in the BED format.
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For detailed information on GMAJ, click here_.
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.. _here: /static/gmaj/docs/gmaj_readme.html
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Gmaj is a tool for viewing and manipulating Generalized Multiple Alignments (GMAs) produced by programs such as TBA (though it can also be used with maf-format alignments from other sources). It can display interactive graphical and text representations of the alignments, a diagram showing the locations of exons and repeats, and other annotations -- all with the user's choice of reference sequence.
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</help>
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</tool> |