annotate macros.xml @ 2:7a12314c5b64 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 97a064489364118d108b0dd2cfb4d9bc53080837-dirty
author iuc
date Thu, 19 Nov 2015 12:32:17 -0500
parents a12ce5668966
children bb7e0ccc0029
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
1 <macros>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
2 <token name="@WRAPPER_VERSION@">2014.11.03.0</token>
1
a12ce5668966 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
parents: 0
diff changeset
3
a12ce5668966 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
parents: 0
diff changeset
4 <xml name="requirements">
a12ce5668966 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
parents: 0
diff changeset
5 <requirements>
2
7a12314c5b64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 97a064489364118d108b0dd2cfb4d9bc53080837-dirty
iuc
parents: 1
diff changeset
6 <requirement type="package" version="2014_11_03">art</requirement>
1
a12ce5668966 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
parents: 0
diff changeset
7 <yield/>
a12ce5668966 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
parents: 0
diff changeset
8 </requirements>
a12ce5668966 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
parents: 0
diff changeset
9 </xml>
a12ce5668966 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
parents: 0
diff changeset
10
0
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
11 <xml name="stdio">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
12 <stdio>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
13 <!-- Anything other than zero is an error -->
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
14 <exit_code range="1:" />
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
15 <exit_code range=":-1" />
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
16 <!-- In case the return code has not been set propery check stderr too -->
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
17 <regex match="Error:" />
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
18 <regex match="Exception:" />
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
19 </stdio>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
20 </xml>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
21 <xml name="aln">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
22 <param type="boolean" label="output ALN alignment file (-a)" name="aln"
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
23 truevalue="-a" falsevalue="" />
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
24 </xml>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
25 <xml name="sam">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
26 <param type="boolean" label="output SAM alignment file (-s)" name="sam"
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
27 truevalue="-s" falsevalue="" />
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
28 </xml>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
29
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
30 <xml name="rndSeed">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
31 <param label="specify a fixed, random seed for the simulation"
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
32 help="Use -1 to request a random seed (-r)" name="rndSeed"
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
33 type="integer" value="-1" optional="true" />
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
34 </xml>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
35
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
36 <xml name="citation">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
37 <citations>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
38 <citation type="doi">10.1093/bioinformatics/btr708</citation>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
39 </citations>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
40 </xml>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
41
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
42 <xml name="amplicon">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
43 <conditional name="amplicon">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
44 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
45 <when value="amplicon_true">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
46 <param label="number of reads per amplicon (for 5'end amplicon sequencing)" name="reads_per_amplicon" type="integer" value="0"/>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
47 </when>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
48 <when value="amplicon_false">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
49 </when>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
50 </conditional>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
51 </xml>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
52
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
53 <xml name="amplicon_pair">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
54 <conditional name="amplicon">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
55 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" />
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
56 <when value="amplicon_true">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
57 <param label="number of read pairs per amplicon (for two-end amplicon sequencing)" name="read_pairs_per_amplicon" type="integer" value="0"/>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
58 </when>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
59 <when value="amplicon_false">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
60 </when>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
61 </conditional>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
62 </xml>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
63
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
64 <xml name="frag_len_sd">
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
65 <param label="the average DNA fragment size"
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
66 name="fragment_size" type="integer" value="200" minimum="101" />
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
67 <param label="the standard deviation of the DNA fragment size"
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
68 name="fragment_sd" type="integer" value="0"/>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
69 </xml>
b98d6fffd00b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff changeset
70 </macros>