root/galaxy-central/tools/emboss_5/emboss_isochore.xml @ 2

リビジョン 2, 2.8 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1<tool id="EMBOSS: isochore47" name="isochore" version="5.0.0">
2  <description>Plots isochores in large DNA sequences</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -outfile $ofile2 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>
5  <!--  <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>-->
6  <inputs>
7    <param format="fasta" name="input1" type="data">
8      <label>Sequences</label>
9    </param>
10    <param name="window" size="4" type="text" value="1000">
11      <label>Window size</label>
12    </param>
13    <param name="shift" size="4" type="text" value="100">
14      <label>Shift increment</label>
15    </param>
16  </inputs>
17  <outputs>
18    <data format="png" name="ofile1" />
19    <data format="isochore" name="ofile2" />
20  </outputs>
21  <!-- <tests>
22    <test>
23      <param name="input1" value="2.fasta"/>
24      <param name="window" value="1000"/>
25      <param name="shift" value="100"/>
26      <output name="ofile1" file="emboss_isochore_out.isochore"/>
27      <output name="ofile2" file="emboss_isochore_out.isochore"/>
28    </test>
29         <test>
30      <param name="input1" value="2.fasta"/>
31      <param name="window" value="1000"/>
32      <param name="shift" value="100"/>
33      <output name="ofile2" file="emboss_isochore_out.isochore"/>
34    </test>
35  </tests>-->
36  <help>
37
38.. class:: warningmark
39
40The input dataset needs to be sequences.
41
42-----
43
44**Syntax**
45
46This application plots GC content over a sequence. It is intended for large sequences such as complete chromosomes or large genomic contigs, although interesting results can also be obtained from shorter sequences. You can view the original documentation here_.   
47
48    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/isochore.html
49
50- Both **Window size** and **Shift increment** are intergers.
51
52-----
53
54**Example**
55
56- Input sequences::
57
58    >hg18_dna range=chrX:151073054-151073376 5'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=none
59    TTTATGTCTATAATCCTTACCAAAAGTTACCTTGGAATAAGAAGAAGTCA
60    GTAAAAAGAAGGCTGTTGTTCCGTGAAATACTGTCTTTATGCCTCAGATT
61    TGGAGTGCTCAGAGCCTCTGCAGCAAAGATTTGGCATGTGTCCTAGGCCT
62    GCTCAGAGCAGCAAATCCCACCCTCTTGGAGAATGAGACTCATAGAGGGA
63    CAGCTCCCTCCTCAGAGGCTTCTCTAATGGGACTCCAAAGAGCAAACACT
64    CAGCCCCATGAGGACTGGCCAGGCCAAGTGGTGTGTGGGAACAGGGAGCA
65    GCGGTTTCCAAGAGGATACAGTA
66
67- Output data file::
68
69    Position    Percent G+C 1 .. 323
70    80  0.422
71    112 0.460
72    144 0.509
73    176 0.534
74    208 0.553
75    240 0.553
76
77- Output graphics file:
78
79.. image:: ../static/emboss_icons/isochore.png
80
81  </help>
82</tool>
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