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comparison tools/emboss_5/emboss_isochore.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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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
40 The input dataset needs to be sequences.
41
42 -----
43
44 **Syntax**
45
46 This 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>