Mercurial > repos > iuc > art
annotate macros.xml @ 6:5c265c4835c0 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 7e2fa670ffad6bf9cd2411d7807c65db7c7e2f6b"
| author | iuc |
|---|---|
| date | Wed, 04 Dec 2019 06:19:06 -0500 |
| parents | ff8599e52a55 |
| children |
| rev | line source |
|---|---|
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0
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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1 <macros> |
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6
5c265c4835c0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 7e2fa670ffad6bf9cd2411d7807c65db7c7e2f6b"
iuc
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2 <token name="@WRAPPER_VERSION@">2016.06.05</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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0
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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
changeset
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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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changeset
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5 <requirements> |
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6
5c265c4835c0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 7e2fa670ffad6bf9cd2411d7807c65db7c7e2f6b"
iuc
parents:
5
diff
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6 <requirement type="package" version="2016.06.05">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
diff
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
diff
changeset
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10 |
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0
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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5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
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22 <param name="aln" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Output ALN alignment file" /> |
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0
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 </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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24 <xml name="sam"> |
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5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
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25 <param name="sam" argument="-s" type="boolean" truevalue="-s" falsevalue="" label="Output SAM alignment file" /> |
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0
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 </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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27 |
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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 name="rndSeed"> |
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5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
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29 <param name="rndSeed" argument="-r" type="integer" value="-1" optional="true" label="Fixed random seed for the simulation" |
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ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
changeset
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30 help="Use -1 to request a random seed" /> |
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0
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 </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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32 |
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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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33 <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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34 <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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35 <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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36 </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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37 </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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38 |
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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 <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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40 <conditional name="amplicon"> |
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5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
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41 <param name="use_amplicon" type="boolean" truevalue="amplicon_true" falsevalue="amplicon_false" label="Run Amplicon Sequencing Simulation" /> |
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0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
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42 <when value="amplicon_true"> |
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5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
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43 <param name="reads_per_amplicon" type="integer" value="0" label="Number of reads per amplicon (for 5'end amplicon sequencing)" /> |
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0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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44 </when> |
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5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
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45 <when value="amplicon_false" /> |
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0
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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46 </conditional> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
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47 </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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48 |
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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 <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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50 <conditional name="amplicon"> |
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5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
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51 <param name="use_amplicon" type="boolean" truevalue="amplicon_true" falsevalue="amplicon_false" label="Run Amplicon Sequencing Simulation" /> |
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0
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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52 <when value="amplicon_true"> |
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5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
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53 <param name="read_pairs_per_amplicon" type="integer" value="0" label="Number of read pairs per amplicon (for two-end amplicon sequencing)" /> |
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0
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 </when> |
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5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
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55 <when value="amplicon_false" /> |
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0
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 </conditional> |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
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57 </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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58 |
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b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
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59 <xml name="frag_len_sd"> |
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5
ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
diff
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60 <param name="fragment_size" type="integer" value="200" label="Average DNA fragment size" /> |
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ff8599e52a55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 1626a4a0313ab6363a214932e6dcd6f54f6ad6cf
iuc
parents:
4
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61 <param name="fragment_sd" type="integer" value="0" label="Standard deviation of the DNA fragment size" /> |
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0
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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62 </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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63 </macros> |