Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/modifySequenceList.xml @ 38:2c0c0a89fad7
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author | m-zytnicki |
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date | Thu, 02 May 2013 09:56:47 -0400 |
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37:d22fadc825e3 | 38:2c0c0a89fad7 |
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1 <tool id="modifySequenceList" name="modify sequence list"> | |
2 <description>Extend or shring a list of sequences. </description> | |
3 <requirements> | |
4 <requirement type="set_environment">PYTHONPATH</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> ../Java/Python/modifySequenceList.py -i $inputFile -f fasta | |
7 #if $OptionStart.Start == "Yes": | |
8 -s $OptionStart.StartVal | |
9 #end if | |
10 #if $OptionEnd.End == "Yes": | |
11 -e $OptionEnd.EndVal | |
12 #end if | |
13 -o $outputFile | |
14 </command> | |
15 | |
16 | |
17 <inputs> | |
18 <param name="inputFile" type="data" format="fasta" label="input file"/> | |
19 | |
20 <conditional name="OptionStart"> | |
21 <param name="Start" type="select" label="keep first nucleotides"> | |
22 <option value="Yes">Yes</option> | |
23 <option value="No" selected="true">No</option> | |
24 </param> | |
25 <when value="Yes"> | |
26 <param name="StartVal" type="integer" value="0" /> | |
27 </when> | |
28 <when value="No"> | |
29 </when> | |
30 </conditional> | |
31 | |
32 <conditional name="OptionEnd"> | |
33 <param name="End" type="select" label="keep last nucleotides"> | |
34 <option value="Yes">Yes</option> | |
35 <option value="No" selected="true">No</option> | |
36 </param> | |
37 <when value="Yes"> | |
38 <param name="EndVal" type="integer" value="0"/> | |
39 </when> | |
40 <when value="No"> | |
41 </when> | |
42 </conditional> | |
43 </inputs> | |
44 | |
45 <outputs> | |
46 <data format="fasta" name="outputFile" label="[modify sequence list] output file"/> | |
47 </outputs> | |
48 | |
49 <help> | |
50 This tool reads a list of sequences (in multi-FASTA/Q format) that you provide and shrinks each sequence to the *n* first nucleotides or the *n* last nucleotides. | |
51 </help> | |
52 </tool> |