root/galaxy-central/tools/emboss_5/emboss_cpgreport.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="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0">
2  <description>Reports all CpG rich regions</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command>cpgreport -sequence $input1 -outfile $out_file1 -outfeat $out_file2 -offormat3 $out_format2 -score $score -auto</command>
5  <inputs>
6    <param format="fasta" name="input1" type="data">
7      <label>On query</label>
8    </param>
9    <param name="score" size="4" type="text" value="17">
10      <label>Score for each CG sequence found (1-200)</label>
11    </param>
12    <param name="out_format2" type="select">
13      <label>Output Feature File Format</label>
14      <option value="gff">GFF</option>
15      <option value="embl">EMBL</option>
16      <option value="swiss">SwissProt</option>
17    </param>
18  </inputs>
19  <outputs>
20    <data format="cpgreport" name="out_file1" />
21    <data format="gff" name="out_file2" />
22  </outputs>
23  <tests>
24    <test>
25      <param name="input1" value="2.fasta"/>
26      <param name="score" value="17"/>
27      <param name="out_format2" value="gff"/>
28      <output name="out_file2" file="emboss_cpgreport_out2.cpgreport"/>
29    </test>
30    <!-- <test>
31      <param name="input1" value="2.fasta"/>
32      <param name="score" value="17"/>
33      <param name="out_format2" value="gff"/>
34      <output name="out_file1" file="emboss_cpgreport_out1.gff"/>
35    </test>  -->
36  </tests>
37  <code file="emboss_format_corrector.py" />
38  <help>
39.. class:: warningmark
40
41The input dataset needs to be sequences.
42
43-----
44
45    You can view the original documentation here_.
46   
47    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgreport.html
48  </help>
49</tool>
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