Mercurial > repos > iuc > art
annotate art_illumina.xml @ 4:531ff1d417b6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
author | iuc |
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date | Fri, 07 Sep 2018 10:57:50 -0400 |
parents | bb7e0ccc0029 |
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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
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1 <tool id="art_illumina" name="ART Illumina" version="2014.11.03.0"> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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2 <description>simulates sequencing data</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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4 <import>macros.xml</import> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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5 </macros> |
1
a12ce5668966
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
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6 <expand macro="requirements"/> |
0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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7 <expand macro="stdio" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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8 <command><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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9 art_illumina |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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10 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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11 #if str($sam) == "-s": |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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12 --samout |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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13 #end if |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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14 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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15 #if not str($aln) == "-a": |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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16 --noALN |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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17 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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18 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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19 #if str($generate.choice) == "paired_end": |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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20 --paired |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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21 --mflen $generate.fragment_size |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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22 --sdev $generate.fragment_sd |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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23 #else if str($generate.choice) == "mate_pair": |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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24 --matepair |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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changeset
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25 --mflen $generate.fragment_size |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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26 --sdev $generate.fragment_sd |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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27 #end if |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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28 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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29 --in $input_seq_file |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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30 --len $read_length |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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31 --fcov $fold_coverage |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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32 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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33 $amplicon |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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34 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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35 --insRate $insRate |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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36 --insRate2 $insRate2 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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37 --delRate $delRate |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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38 --delRate2 $delRate2 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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39 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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40 #if $rndSeed and $rndSeed > -1: |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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41 --rndSeed $rndSeed |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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42 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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43 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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44 --out output; |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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45 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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46 <inputs> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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47 <param label="DNA/RNA reference sequence" format="fasta" name="input_seq_file" type="data"/> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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48 <param label="the fold of read coverage over the reference sequences" name="fold_coverage" type="integer" value="20"/> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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49 <param label="length of reads to be simulated" name="read_length" type="integer" value="100"/> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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50 <param label="amplicon sequencing simulation" name="amplicon" type="boolean" truevalue="--amplicon" falsevalue="" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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51 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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52 <conditional name="generate"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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53 <param name="choice" type="select" label="Type of data to generate"> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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54 <option value="single_end">Single-End</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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55 <option value="paired_end">Paired-End</option> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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56 <option value="mate_pair">Mate-Pair</option> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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57 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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58 <when value="single_end"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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59 </when> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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60 <when value="paired_end"> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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61 <expand macro="frag_len_sd" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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62 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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63 <when value="mate_pair"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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64 <expand macro="frag_len_sd" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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65 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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66 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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67 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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68 <expand macro="aln" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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69 <expand macro="sam" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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70 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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71 <param label="the first-read insertion rate" help="(--insRate)" name="insRate" type="float" value="0.00009" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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72 <param label="the second-read insertion rate" help="(--insRate2)" name="insRate2" type="float" value="0.00015" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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73 <param label="the first-read deletion rate" help="(--delRate)" name="delRate" type="float" value="0.00011" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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74 <param label="the second-read deletion rate" help="(--delRate2)" name="delRate2" type="float" value="0.00023" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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75 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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76 <expand macro="rndSeed" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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77 <!-- todo: id, errfree, masN, qShift(2), sepProf --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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78 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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79 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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80 <!-- Single End --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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81 <data format="fastq" name="output_fq1_single" from_work_dir="output.fq" label="Simulated of Illumina sequencing of $input_seq_file.name"> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
82 <filter>generate['choice'] == "single_end"</filter> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
83 </data> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
84 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
85 <!-- Paired End --> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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86 <data format="fastq" name="output_fq1_paired" from_work_dir="output1.fq" label="Simulated of Illumina sequencing of $input_seq_file.name (Forward)"> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
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87 <filter>generate['choice'] != "single_end"</filter> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
88 </data> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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89 <data format="fastq" name="output_fq2_paired" from_work_dir="output2.fq" label="Simulated of Illumina sequencing of $input_seq_file.name (Reverse)"> |
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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90 <filter>generate['choice'] != "single_end"</filter> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
91 </data> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
92 <data format="sam" name="output_sam" from_work_dir="output.sam" label="Mapping of Simulated Illumina data to $input_seq_file.name"> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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93 <filter>sam</filter> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
94 </data> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
diff
changeset
|
95 |
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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96 <!-- Single End --> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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97 <data format="aln" name="output_aln1_single" from_work_dir="output.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name"> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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98 <filter>aln and generate['choice'] == "single_end"</filter> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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99 </data> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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100 |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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101 <!-- paired end --> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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102 <data format="aln" name="output_aln1_paired" from_work_dir="output1.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name"> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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103 <filter>aln and generate['choice'] != "single_end"</filter> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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104 </data> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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105 <data format="aln" name="output_aln2_paired" from_work_dir="output2.aln" label="Alignment of Simulated Illumina data to $input_seq_file.name"> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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106 <filter>aln and generate['choice'] != "single_end"</filter> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
parents:
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107 </data> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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108 </outputs> |
b98d6fffd00b
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iuc
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109 <tests> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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110 <test> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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111 <param name="rndSeed" value="42" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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112 <param name="input_seq_file" value="input.fa" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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113 <param name="fold_coverage" value="20" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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114 <param name="read_length" value="200" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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115 <param name="choice" value="single_end" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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116 <param name="aln" value="True" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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117 <param name="sam" value="True" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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118 |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
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1
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119 <output name="output_fq1_single" file="art.illumina.01.fq" compare="sim_size" delta="5000" /> |
bb7e0ccc0029
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
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120 <output name="output_aln1_single" file="art.illumina.01.aln" compare="sim_size" delta="5000"/> |
bb7e0ccc0029
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
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1
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121 <output name="output_sam" file="art.illumina.01.sam" compare="sim_size" delta="5000"/> |
0
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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122 </test> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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123 <test> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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124 <param name="rndSeed" value="42" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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125 <param name="input_seq_file" value="input.fa" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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126 <param name="fold_coverage" value="20" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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127 <param name="read_length" value="200" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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128 <param name="choice" value="paired_end" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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129 <param name="fragment_size" value="300" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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130 <param name="fragment_sd" value="10" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
iuc
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131 <param name="aln" value="True" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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132 <param name="sam" value="True" /> |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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133 |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
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1
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134 <output name="output_fq1_paired" file="art.illumina.021.fq" compare="sim_size" delta="5000" /> |
bb7e0ccc0029
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
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135 <output name="output_fq2_paired" file="art.illumina.022.fq" compare="sim_size" delta="5000" /> |
bb7e0ccc0029
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
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136 <output name="output_aln1_paired" file="art.illumina.021.aln" compare="sim_size" delta="5000"/> |
bb7e0ccc0029
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
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137 <output name="output_aln2_paired" file="art.illumina.022.aln" compare="sim_size" delta="5000"/> |
bb7e0ccc0029
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 4f3b019991c8a322870d1130a7c0a34d5c09758f
iuc
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138 <output name="output_sam" file="art.illumina.02.sam" compare="sim_size" delta="5000"/> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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139 </test> |
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140 </tests> |
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141 <help><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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142 Art Illumina Simulator |
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143 ====================== |
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144 |
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145 ART (art_Illumina Q version) is a simulation program to generate sequence read |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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146 data of Illumina sequencers. ART generates reads according to the empirical |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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147 read quality profile summarized from large real read data. ART has been using |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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148 for testing or benchmarking a variety of methods or tools for next-generation |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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149 sequencing data analysis, including read alignment, de novo assembly, detection |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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150 of SNP, CNV, or other structure variation. |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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151 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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152 art_Illumina can generate single-end, paired-end, mate-pair reads, and |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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153 amplicon sequencing simulation of Illumina sequencing platform. Its outputs |
b98d6fffd00b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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154 include FASTQ read, ALN and/or SAM alignment files. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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155 |
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156 ]]></help> |
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157 <expand macro="citation" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/art commit 2b8fe4bffea74c80e20d2d4d0c426cc1631fc05f
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158 </tool> |
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iuc
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159 |