Mercurial > repos > iuc > art
annotate macros.xml @ 4:531ff1d417b6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
| author | iuc |
|---|---|
| date | Fri, 07 Sep 2018 10:57:50 -0400 |
| parents | bb7e0ccc0029 |
| children | ff8599e52a55 |
| rev | line source |
|---|---|
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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1 <macros> |
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3
bb7e0ccc0029
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
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2 <token name="@WRAPPER_VERSION@">3.19.15</token> |
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1
a12ce5668966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
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3 |
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a12ce5668966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
parents:
0
diff
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4 <xml name="requirements"> |
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a12ce5668966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
parents:
0
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5 <requirements> |
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3
bb7e0ccc0029
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
parents:
2
diff
changeset
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6 <requirement type="package" version="3.19.15">art</requirement> |
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1
a12ce5668966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
parents:
0
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changeset
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7 <yield/> |
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a12ce5668966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
parents:
0
diff
changeset
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8 </requirements> |
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a12ce5668966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
parents:
0
diff
changeset
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9 </xml> |
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a12ce5668966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
parents:
0
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10 |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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11 <xml name="stdio"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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12 <stdio> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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13 <!-- Anything other than zero is an error --> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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14 <exit_code range="1:" /> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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15 <exit_code range=":-1" /> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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16 <!-- In case the return code has not been set propery check stderr too --> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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17 <regex match="Error:" /> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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18 <regex match="Exception:" /> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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19 </stdio> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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20 </xml> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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21 <xml name="aln"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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22 <param type="boolean" label="output ALN alignment file (-a)" name="aln" |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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23 truevalue="-a" falsevalue="" /> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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24 </xml> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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25 <xml name="sam"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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26 <param type="boolean" label="output SAM alignment file (-s)" name="sam" |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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27 truevalue="-s" falsevalue="" /> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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28 </xml> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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29 |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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30 <xml name="rndSeed"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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31 <param label="specify a fixed, random seed for the simulation" |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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32 help="Use -1 to request a random seed (-r)" name="rndSeed" |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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33 type="integer" value="-1" optional="true" /> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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34 </xml> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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35 |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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36 <xml name="citation"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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37 <citations> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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38 <citation type="doi">10.1093/bioinformatics/btr708</citation> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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39 </citations> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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40 </xml> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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41 |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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changeset
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42 <xml name="amplicon"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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43 <conditional name="amplicon"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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44 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" /> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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45 <when value="amplicon_true"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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46 <param label="number of reads per amplicon (for 5'end amplicon sequencing)" name="reads_per_amplicon" type="integer" value="0"/> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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47 </when> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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changeset
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48 <when value="amplicon_false"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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49 </when> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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50 </conditional> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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51 </xml> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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52 |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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changeset
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53 <xml name="amplicon_pair"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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54 <conditional name="amplicon"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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55 <param name="use_amplicon" type="boolean" label="Run Amplicon Sequencing Simulation" truevalue="amplicon_true" falsevalue="amplicon_false" /> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
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56 <when value="amplicon_true"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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57 <param label="number of read pairs per amplicon (for two-end amplicon sequencing)" name="read_pairs_per_amplicon" type="integer" value="0"/> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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58 </when> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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changeset
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59 <when value="amplicon_false"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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60 </when> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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61 </conditional> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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62 </xml> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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63 |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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64 <xml name="frag_len_sd"> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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65 <param label="the average DNA fragment size" |
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4
531ff1d417b6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
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66 name="fragment_size" type="integer" value="200" /> |
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0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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67 <param label="the standard deviation of the DNA fragment size" |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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68 name="fragment_sd" type="integer" value="0"/> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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69 </xml> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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70 </macros> |