Mercurial > repos > xuebing > sharplabtool
comparison tools/visualization/LAJ.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="laj_1" name="LAJ"> | |
| 2 <description>Pairwise Alignment Viewer</description> | |
| 3 <command interpreter="python">LAJ.py $maf_input $out_file1</command> | |
| 4 <inputs> | |
| 5 <param name="maf_input" type="data" format="lav" label="Alignment File" optional="False"/> | |
| 6 <param name="seq_file1" type="data" format="fasta" label="First Sequence File" optional="True"/> | |
| 7 <param name="seq_file2" type="data" format="fasta" label="Second Sequence File" optional="True"/> | |
| 8 <param name="exonfile" type="data" format="txt" label="Exon File" optional="True"/> | |
| 9 <param name="repeatfile" type="data" format="txt" label="Repeat File" optional="True"/> | |
| 10 <param name="annotationfile" type="data" format="txt" label="Annotation File" optional="True"/> | |
| 11 <param name="underlayfile" type="data" format="txt" label="Underlay File" optional="True"/> | |
| 12 <param name="highlightfile" type="data" format="txt" label="Highlight File" optional="True"/> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data name="out_file1" format="laj"/> | |
| 16 </outputs> | |
| 17 <help> | |
| 18 You can use this tool to view a set of LAV alignments. You may include FASTA formatted sequences for both species. | |
| 19 | |
| 20 For detailed information on LAJ, click here_. | |
| 21 | |
| 22 .. _here: http://globin.cse.psu.edu/dist/laj/ | |
| 23 | |
| 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. | |
| 25 | |
| 26 .. class:: infomark | |
| 27 | |
| 28 **Note:** If you save output from the applet, you will need to manually refresh your history. | |
| 29 | |
| 30 </help> | |
| 31 <code file="LAJ_code.py"/> | |
| 32 </tool> |