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32 lines
1.7 KiB
XML
32 lines
1.7 KiB
XML
<tool id="laj_1" name="LAJ">
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<description>Pairwise Alignment Viewer</description>
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<command interpreter="python">LAJ.py $maf_input $out_file1</command>
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<inputs>
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<param name="maf_input" type="data" format="lav" label="Alignment File" optional="False"/>
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<param name="seq_file1" type="data" format="fasta" label="First Sequence File" optional="True"/>
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<param name="seq_file2" type="data" format="fasta" label="Second Sequence File" optional="True"/>
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<param name="exonfile" type="data" format="txt" label="Exon File" optional="True"/>
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<param name="repeatfile" type="data" format="txt" label="Repeat File" optional="True"/>
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<param name="annotationfile" type="data" format="txt" label="Annotation File" optional="True"/>
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<param name="underlayfile" type="data" format="txt" label="Underlay File" optional="True"/>
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<param name="highlightfile" type="data" format="txt" label="Highlight File" optional="True"/>
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</inputs>
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<outputs>
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<data name="out_file1" format="laj"/>
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</outputs>
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<help>
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You can use this tool to view a set of LAV alignments. You may include FASTA formatted sequences for both species.
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For detailed information on LAJ, click here_.
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.. _here: http://globin.cse.psu.edu/dist/laj/
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Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to other web sites containing additional information about particular regions.
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.. class:: infomark
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**Note:** If you save output from the applet, you will need to manually refresh your history.
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</help>
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<code file="LAJ_code.py"/>
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</tool> |