root/galaxy-central/tools/visualization/LAJ.xml

リビジョン 2, 1.7 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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>
18You can use this tool to view a set of LAV alignments.  You may include FASTA formatted sequences for both species.
19
20For detailed information on LAJ, click here_.
21
22.. _here: http://globin.cse.psu.edu/dist/laj/
23
24Laj 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>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。