Mercurial > repos > iuc > art
annotate macros.xml @ 6:52b84f4bac10 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
| author | iuc |
|---|---|
| date | Mon, 30 Nov 2015 21:46:20 -0500 |
| parents | 7d6f5eef1245 |
| children | 3f163b178c5c |
| rev | line source |
|---|---|
| 0 | 1 <macros> |
| 2 <token name="@WRAPPER_VERSION@">2014.11.03.0</token> | |
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7d6f5eef1245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 321bb0b81c749a898c0b59447a5a87d68c4dd058
iuc
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3 |
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7d6f5eef1245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 321bb0b81c749a898c0b59447a5a87d68c4dd058
iuc
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4 <xml name="requirements"> |
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7d6f5eef1245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 321bb0b81c749a898c0b59447a5a87d68c4dd058
iuc
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5 <requirements> |
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6
52b84f4bac10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
iuc
parents:
5
diff
changeset
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6 <requirement type="package" version="2014_11_03">art</requirement> |
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5
7d6f5eef1245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 321bb0b81c749a898c0b59447a5a87d68c4dd058
iuc
parents:
0
diff
changeset
|
7 <yield/> |
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7d6f5eef1245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 321bb0b81c749a898c0b59447a5a87d68c4dd058
iuc
parents:
0
diff
changeset
|
8 </requirements> |
|
7d6f5eef1245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 321bb0b81c749a898c0b59447a5a87d68c4dd058
iuc
parents:
0
diff
changeset
|
9 </xml> |
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7d6f5eef1245
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 321bb0b81c749a898c0b59447a5a87d68c4dd058
iuc
parents:
0
diff
changeset
|
10 |
| 0 | 11 <xml name="stdio"> |
| 12 <stdio> | |
| 13 <!-- Anything other than zero is an error --> | |
| 14 <exit_code range="1:" /> | |
| 15 <exit_code range=":-1" /> | |
| 16 <!-- In case the return code has not been set propery check stderr too --> | |
| 17 <regex match="Error:" /> | |
| 18 <regex match="Exception:" /> | |
| 19 </stdio> | |
| 20 </xml> | |
| 21 <xml name="aln"> | |
| 22 <param type="boolean" label="output ALN alignment file (-a)" name="aln" | |
| 23 truevalue="-a" falsevalue="" /> | |
| 24 </xml> | |
| 25 <xml name="sam"> | |
| 26 <param type="boolean" label="output SAM alignment file (-s)" name="sam" | |
| 27 truevalue="-s" falsevalue="" /> | |
| 28 </xml> | |
| 29 | |
| 30 <xml name="rndSeed"> | |
| 31 <param label="specify a fixed, random seed for the simulation" | |
| 32 help="Use -1 to request a random seed (-r)" name="rndSeed" | |
| 33 type="integer" value="-1" optional="true" /> | |
| 34 </xml> | |
| 35 | |
| 36 <xml name="citation"> | |
| 37 <citations> | |
| 38 <citation type="doi">10.1093/bioinformatics/btr708</citation> | |
| 39 </citations> | |
| 40 </xml> | |
| 41 | |
| 42 <xml name="amplicon"> | |
| 43 <conditional name="amplicon"> | |
| 44 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" /> | |
| 45 <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"/> | |
| 47 </when> | |
| 48 <when value="amplicon_false"> | |
| 49 </when> | |
| 50 </conditional> | |
| 51 </xml> | |
| 52 | |
| 53 <xml name="amplicon_pair"> | |
| 54 <conditional name="amplicon"> | |
| 55 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" /> | |
| 56 <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"/> | |
| 58 </when> | |
| 59 <when value="amplicon_false"> | |
| 60 </when> | |
| 61 </conditional> | |
| 62 </xml> | |
| 63 | |
| 64 <xml name="frag_len_sd"> | |
| 65 <param label="the average DNA fragment size" | |
| 66 name="fragment_size" type="integer" value="200" minimum="101" /> | |
| 67 <param label="the standard deviation of the DNA fragment size" | |
| 68 name="fragment_sd" type="integer" value="0"/> | |
| 69 </xml> | |
| 70 </macros> |