root/galaxy-central/tools/emboss_5/emboss_est2genome.xml

リビジョン 2, 4.1 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0">
2  <description>Align EST and genomic DNA sequences</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty
5  $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command>
6  <inputs>
7    <param format="fasta" name="input1" type="data">
8      <label>EST sequence(s)</label>
9    </param>
10    <param format="data" name="input2" type="data">
11      <label>Genomic sequence</label>
12    </param>
13    <param name="match" size="4" type="text" value="1">
14      <label>Score for matching two bases</label>
15    </param>
16    <param name="mismatch" size="4" type="text" value="1">
17      <label>Cost for mismatching two bases</label>
18    </param>
19    <param name="gappenalty" size="4" type="text" value="2">
20      <label>Cost for deleting a single base in either sequence, excluding introns</label>
21    </param>
22    <param name="intronpenalty" size="4" type="text" value="40">
23      <label>Cost for an intron, independent of length</label>
24    </param>
25    <param name="splicepenalty" size="4" type="text" value="20">
26      <label>Cost for an intron, independent of length and starting/ending on donor-acceptor sites</label>
27    </param>
28    <param name="minscore" size="4" type="text" value="30">
29      <label>Exclude alignments with scores below this threshold score</label>
30    </param>
31    <param name="reverse" type="select">
32      <label>Reverse the orientation of the EST sequence</label>
33      <option value="no">No</option>
34      <option value="yes">Yes</option>
35    </param>
36    <param name="splice" type="select">
37      <label>Use donor and acceptor splice sites</label>
38      <option value="yes">Yes</option>
39      <option value="no">No</option>
40    </param>
41    <param name="mode" type="select">
42      <label>Comparison mode</label>
43      <option value="both">Both strands</option>
44      <option value="forward">Forward strand only</option>
45      <option value="reverse">Reverse strand only</option>
46    </param>
47    <param name="best" type="select">
48      <label>Only best comparisons</label>
49      <option value="yes">Yes</option>
50      <option value="no">No</option>
51    </param>
52    <param name="shuffle" size="4" type="text" value="0">
53      <label>Shuffle</label>
54    </param>
55    <param name="seed" size="4" type="text" value="20825">
56      <label>Random number seed</label>
57    </param>
58    <param name="align" type="select">
59      <label>Show the alignment</label>
60      <option value="no">No</option>
61      <option value="yes">Yes</option>
62    </param>
63    <param name="width" size="4" type="text" value="50">
64      <label>Alignment width</label>
65    </param>
66  </inputs>
67  <outputs>
68    <data format="est2genome" name="out_file1" />
69  </outputs>
70  <tests>
71    <test>
72      <param name="input1" value="2.fasta"/>
73      <param name="input2" value="1.fasta"/>
74      <param name="match" value="1"/>
75      <param name="mismatch" value="1"/>
76      <param name="match" value="1"/>
77      <param name="gappenalty" value="2"/>
78      <param name="intronpenalty" value="40"/>
79      <param name="splicepenalty" value="20"/>
80      <param name="minscore" value="30"/>
81      <param name="reverse" value="no"/>
82      <param name="splice" value="yes"/>
83      <param name="mode" value="both"/>
84      <param name="best" value="yes"/>
85      <param name="shuffle" value="0"/>
86      <param name="seed" value="20825"/>
87      <param name="align" value="no"/>
88      <param name="width" value="50"/>
89      <output name="out_file1" file="emboss_est2genome_out.est2genome"/>
90    </test>
91  </tests>
92  <help>
93.. class:: warningmark
94
95The input dataset needs to be sequences.
96
97-----
98
99    You can view the original documentation here_.
100   
101    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/est2genome.html
102  </help>
103</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。