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46 lines
2.0 KiB
XML
46 lines
2.0 KiB
XML
<tool id="laj_1" name="LAJ" version="1.0.0">
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<description>Pairwise Alignment Viewer</description>
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<code file="LAJ_code.py"/>
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<command><![CDATA[
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python '$__tool_directory__/LAJ.py' '$maf_input' '$out_file1'
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]]></command>
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<inputs>
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<param name="maf_input" type="data" format="lav" label="Alignment File"/>
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<param name="seq_file1" type="data" format="fasta" optional="true" label="First Sequence File"/>
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<param name="seq_file2" type="data" format="fasta" optional="true" label="Second Sequence File"/>
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<param name="exonfile" type="data" format="txt" optional="true" label="Exon File"/>
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<param name="repeatfile" type="data" format="txt" optional="true" label="Repeat File"/>
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<param name="annotationfile" type="data" format="txt" optional="true" label="Annotation File"/>
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<param name="underlayfile" type="data" format="txt" optional="true" label="Underlay File"/>
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<param name="highlightfile" type="data" format="txt" optional="true" label="Highlight File"/>
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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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<tests>
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</tests>
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<help><![CDATA[
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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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<citations>
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<citation type="bibtex">
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@misc{Miller2005,
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author = {Miller Lab},
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year = {2005},
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title = {Laj},
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url = {http://globin.bx.psu.edu/dist/laj/},
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}
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</citation>
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</citations>
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</tool>
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