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1 <tool id="laj_1" name="LAJ">
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2 <description>Pairwise Alignment Viewer</description>
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3 <command interpreter="python">LAJ.py $maf_input $out_file1</command>
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4 <inputs>
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5 <param name="maf_input" type="data" format="lav" label="Alignment File" optional="False"/>
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6 <param name="seq_file1" type="data" format="fasta" label="First Sequence File" optional="True"/>
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7 <param name="seq_file2" type="data" format="fasta" label="Second Sequence File" optional="True"/>
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8 <param name="exonfile" type="data" format="txt" label="Exon File" optional="True"/>
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9 <param name="repeatfile" type="data" format="txt" label="Repeat File" optional="True"/>
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10 <param name="annotationfile" type="data" format="txt" label="Annotation File" optional="True"/>
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11 <param name="underlayfile" type="data" format="txt" label="Underlay File" optional="True"/>
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12 <param name="highlightfile" type="data" format="txt" label="Highlight File" optional="True"/>
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13 </inputs>
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14 <outputs>
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15 <data name="out_file1" format="laj"/>
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16 </outputs>
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17 <help>
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18 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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19
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20 For detailed information on LAJ, click here_.
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21
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22 .. _here: http://globin.cse.psu.edu/dist/laj/
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23
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24 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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25
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26 .. class:: infomark
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27
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28 **Note:** If you save output from the applet, you will need to manually refresh your history.
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29
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30 </help>
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31 <code file="LAJ_code.py"/>
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32 </tool> |
