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comparison SMART/galaxy/modifySequenceList.xml @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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35:d94018ca4ada 36:44d5973c188c
1 <tool id="modifySequenceList" name="modify sequence list">
2 <description>Extend or shring a list of sequences. </description>
3 <command interpreter="python"> ../Java/Python/modifySequenceList.py -i $inputFile -f fasta
4 #if $OptionStart.Start == "Yes":
5 -s $OptionStart.StartVal
6 #end if
7 #if $OptionEnd.End == "Yes":
8 -e $OptionEnd.EndVal
9 #end if
10 -o $outputFile
11 </command>
12
13
14 <inputs>
15 <param name="inputFile" type="data" format="fasta" label="input file"/>
16
17 <conditional name="OptionStart">
18 <param name="Start" type="select" label="keep first nucleotides">
19 <option value="Yes">Yes</option>
20 <option value="No" selected="true">No</option>
21 </param>
22 <when value="Yes">
23 <param name="StartVal" type="integer" value="0" />
24 </when>
25 <when value="No">
26 </when>
27 </conditional>
28
29 <conditional name="OptionEnd">
30 <param name="End" type="select" label="keep last nucleotides">
31 <option value="Yes">Yes</option>
32 <option value="No" selected="true">No</option>
33 </param>
34 <when value="Yes">
35 <param name="EndVal" type="integer" value="0"/>
36 </when>
37 <when value="No">
38 </when>
39 </conditional>
40 </inputs>
41
42 <outputs>
43 <data format="fasta" name="outputFile" label="[modifySequenceList] Output File"/>
44 </outputs>
45
46 <help>
47 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.
48 </help>
49 </tool>