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comparison macros.xml @ 5:ff8599e52a55 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
author iuc
date Thu, 11 Apr 2019 03:22:40 -0400
parents 531ff1d417b6
children 5c265c4835c0
comparison
equal deleted inserted replaced
4:531ff1d417b6 5:ff8599e52a55
17 <regex match="Error:" /> 17 <regex match="Error:" />
18 <regex match="Exception:" /> 18 <regex match="Exception:" />
19 </stdio> 19 </stdio>
20 </xml> 20 </xml>
21 <xml name="aln"> 21 <xml name="aln">
22 <param type="boolean" label="output ALN alignment file (-a)" name="aln" 22 <param name="aln" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Output ALN alignment file" />
23 truevalue="-a" falsevalue="" />
24 </xml> 23 </xml>
25 <xml name="sam"> 24 <xml name="sam">
26 <param type="boolean" label="output SAM alignment file (-s)" name="sam" 25 <param name="sam" argument="-s" type="boolean" truevalue="-s" falsevalue="" label="Output SAM alignment file" />
27 truevalue="-s" falsevalue="" />
28 </xml> 26 </xml>
29 27
30 <xml name="rndSeed"> 28 <xml name="rndSeed">
31 <param label="specify a fixed, random seed for the simulation" 29 <param name="rndSeed" argument="-r" type="integer" value="-1" optional="true" label="Fixed random seed for the simulation"
32 help="Use -1 to request a random seed (-r)" name="rndSeed" 30 help="Use -1 to request a random seed" />
33 type="integer" value="-1" optional="true" />
34 </xml> 31 </xml>
35 32
36 <xml name="citation"> 33 <xml name="citation">
37 <citations> 34 <citations>
38 <citation type="doi">10.1093/bioinformatics/btr708</citation> 35 <citation type="doi">10.1093/bioinformatics/btr708</citation>
39 </citations> 36 </citations>
40 </xml> 37 </xml>
41 38
42 <xml name="amplicon"> 39 <xml name="amplicon">
43 <conditional name="amplicon"> 40 <conditional name="amplicon">
44 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" /> 41 <param name="use_amplicon" type="boolean" truevalue="amplicon_true" falsevalue="amplicon_false" label="Run Amplicon Sequencing Simulation" />
45 <when value="amplicon_true"> 42 <when value="amplicon_true">
46 <param label="number of reads per amplicon (for 5'end amplicon sequencing)" name="reads_per_amplicon" type="integer" value="0"/> 43 <param name="reads_per_amplicon" type="integer" value="0" label="Number of reads per amplicon (for 5'end amplicon sequencing)" />
47 </when> 44 </when>
48 <when value="amplicon_false"> 45 <when value="amplicon_false" />
49 </when>
50 </conditional> 46 </conditional>
51 </xml> 47 </xml>
52 48
53 <xml name="amplicon_pair"> 49 <xml name="amplicon_pair">
54 <conditional name="amplicon"> 50 <conditional name="amplicon">
55 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" /> 51 <param name="use_amplicon" type="boolean" truevalue="amplicon_true" falsevalue="amplicon_false" label="Run Amplicon Sequencing Simulation" />
56 <when value="amplicon_true"> 52 <when value="amplicon_true">
57 <param label="number of read pairs per amplicon (for two-end amplicon sequencing)" name="read_pairs_per_amplicon" type="integer" value="0"/> 53 <param name="read_pairs_per_amplicon" type="integer" value="0" label="Number of read pairs per amplicon (for two-end amplicon sequencing)" />
58 </when> 54 </when>
59 <when value="amplicon_false"> 55 <when value="amplicon_false" />
60 </when>
61 </conditional> 56 </conditional>
62 </xml> 57 </xml>
63 58
64 <xml name="frag_len_sd"> 59 <xml name="frag_len_sd">
65 <param label="the average DNA fragment size" 60 <param name="fragment_size" type="integer" value="200" label="Average DNA fragment size" />
66 name="fragment_size" type="integer" value="200" /> 61 <param name="fragment_sd" type="integer" value="0" label="Standard deviation of the DNA fragment size" />
67 <param label="the standard deviation of the DNA fragment size"
68 name="fragment_sd" type="integer" value="0"/>
69 </xml> 62 </xml>
70 </macros> 63 </macros>