Mercurial > repos > iuc > art
annotate macros.xml @ 5:ff8599e52a55 draft
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 |
| 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> |
|
3
bb7e0ccc0029
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
parents:
2
diff
changeset
|
2 <token name="@WRAPPER_VERSION@">3.19.15</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> |
|
3
bb7e0ccc0029
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
parents:
2
diff
changeset
|
6 <requirement type="package" version="3.19.15">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"> |
|
5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
|
22 <param name="aln" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Output ALN alignment file" /> |
|
0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
23 </xml> |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
24 <xml name="sam"> |
|
5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
|
25 <param name="sam" argument="-s" type="boolean" truevalue="-s" falsevalue="" label="Output SAM alignment file" /> |
|
0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
26 </xml> |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
27 |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
28 <xml name="rndSeed"> |
|
5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
|
29 <param name="rndSeed" argument="-r" type="integer" value="-1" optional="true" label="Fixed random seed for the simulation" |
|
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
|
30 help="Use -1 to request a random seed" /> |
|
0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
31 </xml> |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
32 |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
33 <xml name="citation"> |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
34 <citations> |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
35 <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
|
36 </citations> |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
37 </xml> |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
38 |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
39 <xml name="amplicon"> |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
40 <conditional name="amplicon"> |
|
5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
|
41 <param name="use_amplicon" type="boolean" truevalue="amplicon_true" falsevalue="amplicon_false" label="Run Amplicon Sequencing Simulation" /> |
|
0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
42 <when value="amplicon_true"> |
|
5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
|
43 <param name="reads_per_amplicon" type="integer" value="0" label="Number of reads per amplicon (for 5'end amplicon sequencing)" /> |
|
0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
44 </when> |
|
5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
|
45 <when value="amplicon_false" /> |
|
0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
46 </conditional> |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
47 </xml> |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
48 |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
49 <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
|
50 <conditional name="amplicon"> |
|
5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
|
51 <param name="use_amplicon" type="boolean" truevalue="amplicon_true" falsevalue="amplicon_false" label="Run Amplicon Sequencing Simulation" /> |
|
0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
52 <when value="amplicon_true"> |
|
5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
|
53 <param name="read_pairs_per_amplicon" type="integer" value="0" label="Number of read pairs per amplicon (for two-end amplicon sequencing)" /> |
|
0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
54 </when> |
|
5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
|
55 <when value="amplicon_false" /> |
|
0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
56 </conditional> |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
57 </xml> |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
58 |
|
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
59 <xml name="frag_len_sd"> |
|
5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
|
60 <param name="fragment_size" type="integer" value="200" label="Average DNA fragment size" /> |
|
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
|
61 <param name="fragment_sd" type="integer" value="0" label="Standard deviation of the DNA fragment size" /> |
|
0
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 </macros> |