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comparison macros.xml @ 0:03a48ad6b460 draft

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author iuc
date Fri, 10 Apr 2015 22:46:25 -0400
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children 7d6f5eef1245
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-1:000000000000 0:03a48ad6b460
1 <macros>
2 <token name="@WRAPPER_VERSION@">2014.11.03.0</token>
3 <xml name="stdio">
4 <stdio>
5 <!-- Anything other than zero is an error -->
6 <exit_code range="1:" />
7 <exit_code range=":-1" />
8 <!-- In case the return code has not been set propery check stderr too -->
9 <regex match="Error:" />
10 <regex match="Exception:" />
11 </stdio>
12 </xml>
13 <xml name="aln">
14 <param type="boolean" label="output ALN alignment file (-a)" name="aln"
15 truevalue="-a" falsevalue="" />
16 </xml>
17 <xml name="sam">
18 <param type="boolean" label="output SAM alignment file (-s)" name="sam"
19 truevalue="-s" falsevalue="" />
20 </xml>
21
22 <xml name="rndSeed">
23 <param label="specify a fixed, random seed for the simulation"
24 help="Use -1 to request a random seed (-r)" name="rndSeed"
25 type="integer" value="-1" optional="true" />
26 </xml>
27
28 <xml name="citation">
29 <citations>
30 <citation type="doi">10.1093/bioinformatics/btr708</citation>
31 </citations>
32 </xml>
33
34 <xml name="amplicon">
35 <conditional name="amplicon">
36 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
37 <when value="amplicon_true">
38 <param label="number of reads per amplicon (for 5'end amplicon sequencing)" name="reads_per_amplicon" type="integer" value="0"/>
39 </when>
40 <when value="amplicon_false">
41 </when>
42 </conditional>
43 </xml>
44
45 <xml name="amplicon_pair">
46 <conditional name="amplicon">
47 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
48 <when value="amplicon_true">
49 <param label="number of read pairs per amplicon (for two-end amplicon sequencing)" name="read_pairs_per_amplicon" type="integer" value="0"/>
50 </when>
51 <when value="amplicon_false">
52 </when>
53 </conditional>
54 </xml>
55
56 <xml name="frag_len_sd">
57 <param label="the average DNA fragment size"
58 name="fragment_size" type="integer" value="200" minimum="101" />
59 <param label="the standard deviation of the DNA fragment size"
60 name="fragment_sd" type="integer" value="0"/>
61 </xml>
62 </macros>