Mercurial > repos > iuc > trinity

annotate trinity.xml @ 28:7f916fe93c16 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
author iuc
date Wed, 12 May 2021 08:41:44 +0000
parents 20fb86e85c0f
children e8aca4d11bc0
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20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 23
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1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@+galaxy1">
0
1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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2 <description>de novo assembly of RNA-Seq data</description>
11
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iuc
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3 <macros>
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
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4 <import>macros.xml</import>
80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
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5 </macros>
16
7c21b4380e84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
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6 <expand macro="requirements" />
7c21b4380e84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
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7 <command detect_errors="aggressive"><![CDATA[
20
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iuc
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8 if [ -z "\$GALAXY_MEMORY_MB" ] ; then
875e118b5f1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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9 GALAXY_MEMORY_GB=1 ;
875e118b5f1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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10 else
875e118b5f1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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11 GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
875e118b5f1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
parents: 19
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12 fi ;
875e118b5f1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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13
875e118b5f1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
parents: 19
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14 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
875e118b5f1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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15 workdir=`pwd` ;
875e118b5f1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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16 cd "\$TRINITY_SCRATCH_DIR" ;
875e118b5f1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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17 fi ;
875e118b5f1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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18
19
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iuc
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19 #if $additional_params.guided.is_guided == "yes":
f07bc380d66c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
iuc
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20 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
f07bc380d66c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
iuc
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21 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&
f07bc380d66c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
iuc
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22 #end if
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iuc
parents: 27
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23 #if $pool.pool_mode == "Yes":
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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24 #if str($pool.inputs.paired_or_single) == "single":
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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25 #for i, f in enumerate($pool.inputs.input):
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
parents: 27
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26 ln -s '$f' input${i}.${f.ext} &&
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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27 #end for
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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28 #elif str($pool.inputs.paired_or_single) == "paired":
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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29 #for i, f in enumerate($pool.inputs.left_input):
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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30 ln -s '$f' left_input${i}.${f.ext} &&
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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31 #end for
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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32 #for i, f in enumerate($pool.inputs.right_input):
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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33 ln -s '$f' right_input${i}.${f.ext} &&
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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34 #end for
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
parents: 27
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35 #elif str($pool.inputs.paired_or_single) == "paired_collection":
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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36 #for i, f in enumerate($pool.inputs.pair_input):
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
parents: 27
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37 ln -s '$f.forward' 'left_input${i}.${f.forward.ext}' &&
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
parents: 27
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38 ln -s '$f.reverse' 'right_input${i}.${f.reverse.ext}' &&
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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39 #end for
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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40 #end if
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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41 #elif $pool.pool_mode == "No":
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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42 #if $pool.inputs.paired_or_single == "unmerged_paired_collection":
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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43 ln -s '$pool.inputs.pair_input.forward' 'left_input.${$pool.inputs.pair_input.forward.ext}' &&
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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44 ln -s '$pool.inputs.pair_input.reverse' 'right_input.${pool.inputs.pair_input.reverse.ext}' &&
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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parents: 27
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45 #elif $pool.inputs.paired_or_single == "unmerged_single_collection":
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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46 ln -s '$pool.inputs.input' 'input.${pool.inputs.input.ext}' &&
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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47 #end if
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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48 #end if
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49
19
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50 Trinity --no_version_check
0
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51
21
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52 ## Inputs
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53 #if $pool.pool_mode == "Yes":
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54 #if str($pool.inputs.paired_or_single) == "single":
28
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55 --single ${ ','.join(["'input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.input)]) }
21
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56 #if $pool.inputs.input[0].is_of_type('fasta'):
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57 --seqType fa
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58 #else:
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59 --seqType fq
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60 #end if
3
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61
21
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62 #if $pool.inputs.strand.is_strand_specific:
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63 --SS_lib_type $pool.inputs.strand.library_type
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64 #end if
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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65 #elif str($pool.inputs.paired_or_single) == "paired":
28
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66 --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.left_input)]) }
3
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67
28
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68 --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.right_input)]) }
18
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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69
21
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70 #if $pool.inputs.left_input[0].is_of_type('fasta'):
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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71 --seqType fa
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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72 #else:
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73 --seqType fq
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74 #end if
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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75 @COMMAND_PAIRED_STRAND_JACCARD@
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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76 #elif str($pool.inputs.paired_or_single) == "paired_collection":
28
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77 --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.forward.ext) for i, f in enumerate($pool.inputs.pair_input)]) }
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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78 --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.reverse.ext) for i, f in enumerate($pool.inputs.pair_input)]) }
21
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iuc
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79 #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'):
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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80 --seqType fa
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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81 #else:
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82 --seqType fq
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83 #end if
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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84 @COMMAND_PAIRED_STRAND_JACCARD@
0
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85 #end if
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86 #elif $pool.pool_mode == "No":
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87 #if $pool.inputs.paired_or_single == "unmerged_paired_collection":
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88 --left 'left_input.${$pool.inputs.pair_input.forward.ext}'
0
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89
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90 --right 'right_input.${pool.inputs.pair_input.reverse.ext}'
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91
21
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92 #if $pool.inputs.pair_input.forward.is_of_type('fasta'):
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93 --seqType fa
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94 #else:
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95 --seqType fq
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96 #end if
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97 @COMMAND_PAIRED_STRAND_JACCARD@
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98 #elif $pool.inputs.paired_or_single == "unmerged_single_collection":
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99 --single 'input.${pool.inputs.input.ext}'
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100
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101 #if $pool.inputs.input.is_of_type('fasta'):
21
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102 --seqType fa
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103 #else:
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104 --seqType fq
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105 #end if
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106
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107 #if $pool.inputs.strand.is_strand_specific:
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108 --SS_lib_type $pool.inputs.strand.library_type
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109 #end if
0
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110 #end if
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111 #end if
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112 $norm
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113
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114 ## Additional parameters.
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115 #if $additional_params.min_contig_length:
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116 --min_contig_length $additional_params.min_contig_length
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117 #end if
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118 #if $additional_params.long_reads:
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119 --long_reads $additional_params.long_reads
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120 #end if
1
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121 #if $additional_params.guided.is_guided == "yes":
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122 --genome_guided_bam 'localbam.bam'
0
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123
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124 #if $additional_params.guided.genome_guided_min_coverage:
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125 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
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126 #end if
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127
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128 #if $additional_params.guided.genome_guided_min_reads_per_partition:
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129 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
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130 #end if
3
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131
19
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132 #if $additional_params.guided.genome_guided_max_intron:
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133 --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron
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134 #end if
0
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135 #end if
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136
11
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137 #if $additional_params.min_kmer_cov:
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138 --min_kmer_cov $additional_params.min_kmer_cov
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139 #end if
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140
0
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141 ## CPU and butterfly options.
20
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142 --CPU \${GALAXY_SLOTS:-4} --max_memory \${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax \${GALAXY_MEMORY_GB:-1}G --bfly_opts '-V 10 --stderr'
3
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143
2
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144 ## > $trinity_log 2>&1
20
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145
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146 &&
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147
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148 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
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149 mkdir -p "\$workdir/trinity_out_dir";
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150 cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir";
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151 cd "\$workdir";
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152 fi ;
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153
0
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154 ]]></command>
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155 <inputs>
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156 <conditional name="pool">
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157 <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" >
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158 <option value="No">No</option>
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159 <option value="Yes" selected="True">Yes</option>
0
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160 </param>
21
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161 <when value="Yes" >
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162 <conditional name="inputs">
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163 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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164 <option value="single" selected="true">Single-end</option>
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165 <option value="paired">Paired-end</option>
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166 <option value="paired_collection">Paired-end collection</option>
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167 </param>
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168 <when value="single">
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169 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Single-end reads" help=""/>
21
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170 <conditional name="strand">
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171 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
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172 <when value="false">
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173 </when>
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parents: 20
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174 <when value="true">
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175 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
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176 <option value="F">F</option>
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177 <option value="R">R</option>
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178 </param>
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179 </when>
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180 </conditional>
0
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181 </when>
21
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182 <when value="paired">
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183 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Left/Forward strand reads" />
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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184 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Right/Reverse strand reads" />
21
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185 <expand macro="input_paired_strand_jaccard" />
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186 </when>
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187 <when value="paired_collection">
27
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188 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger,fastqsanger.gz" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/>
21
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189 <expand macro="input_paired_strand_jaccard" />
0
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190 </when>
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191 </conditional>
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192 </when>
21
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parents: 20
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193 <when value="No">
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194 <conditional name="inputs">
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195 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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196 <option value="unmerged_single_collection">Single-end</option>
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197 <option value="unmerged_paired_collection">Paired-end</option>
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198 </param>
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199 <when value="unmerged_single_collection">
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200 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Single-end reads" help="Elements of collection will NOT be merged"/>
21
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201 <conditional name="strand">
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202 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
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parents: 20
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203 <when value="false">
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204 </when>
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parents: 20
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205 <when value="true">
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206 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
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207 <option value="F">F</option>
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208 <option value="R">R</option>
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209 </param>
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210 </when>
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211 </conditional>
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212 </when>
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213 <when value="unmerged_paired_collection">
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214 <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger,fastqsanger.gz" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/>
21
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215 <expand macro="input_paired_strand_jaccard" />
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216 </when>
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217 </conditional>
18
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parents: 16
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218 </when>
0
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219 </conditional>
23
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220 <param name="norm" type="boolean" argument="--no_normalize_reads" truevalue="" falsevalue="--no_normalize_reads" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
0
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221 <section name="additional_params" title="Additional Options" expanded="False">
11
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222 <param name="min_contig_length" argument="--min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
3
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223
0
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224 <conditional name="guided">
1
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225 <param name="is_guided" type="select" label="Use the genome guided mode?" help="If you already mapped the reads to the genome, Trinity can use this information">
0
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226 <option value="no">No</option>
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227 <option value="yes">Yes</option>
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228 </param>
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229 <when value="no">
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230 </when>
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231 <when value="yes">
19
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232 <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
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233 <param name="genome_guided_max_intron" argument="--genome_guided_max_intron" type="integer" value="" min="1" label="Maximum allowed intron length (also maximum fragment span on genome)"/>
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234 <param name="genome_guided_min_coverage" argument="--genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
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235 <param name="genome_guided_min_reads_per_partition" argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
0
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236 </when>
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237 </conditional>
3
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parents: 2
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238
18
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239 <param name="long_reads" argument="--long_reads" type="data" format="fasta" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
3
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240
11
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241 <param name="min_kmer_cov" argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
0
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242 </section>
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243 </inputs>
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244 <outputs>
18
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245 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
21
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246 <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map" from_work_dir="trinity_out_dir/Trinity.fasta.gene_trans_map"/>
0
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247 </outputs>
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248 <tests>
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249 <test>
21
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250 <param name="pool_mode" value="No" />
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251 <param name="paired_or_single" value="unmerged_paired_collection"/>
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252 <param name="pair_input">
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253 <collection type="paired">
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254 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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255 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 23
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256 </collection>
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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257 </param>
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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258 <param name="is_strand_specific" value="true"/>
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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259 <param name="norm" value="true"/>
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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260 <param name="library_type" value="RF"/>
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 23
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261 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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262 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" />
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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263 </test>
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 23
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264 <test>
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 23
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265 <param name="pool_mode" value="No" />
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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266 <param name="paired_or_single" value="unmerged_paired_collection"/>
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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267 <param name="pair_input">
20fb86e85c0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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268 <collection type="paired">
28
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iuc
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269 <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger.gz" />
7f916fe93c16 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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270 <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger.gz" />
21
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271 </collection>
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iuc
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272 </param>
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iuc
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273 <param name="is_strand_specific" value="true"/>
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 20
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274 <param name="norm" value="true"/>
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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275 <param name="library_type" value="RF"/>
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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276 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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277 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" />
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278 </test>
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iuc
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279 <test>
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iuc
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280 <param name="pool_mode" value="No" />
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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281 <param name="paired_or_single" value="unmerged_single_collection"/>
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iuc
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282 <param name="input" value="reads.left.fq" ftype="fastqsanger"/>
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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283 <param name="is_strand_specific" value="true"/>
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 20
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284 <param name="norm" value="false"/>
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 20
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285 <param name="library_type" value="F"/>
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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286 <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" />
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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287 <output name="gene_to_trans" file="raw/Trinity_single_unmerged_1.map" compare="sim_size" />
3867ecd957f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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288 </test>
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iuc
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289 <test>
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iuc
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290 <param name="pool_mode" value="Yes" />
0
1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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291 <param name="paired_or_single" value="paired"/>
3
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iuc
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292 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
8ffafd84a7b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 72247137f912b62dd5a3bc566524988bce10b515
iuc
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293 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
0
1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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294 <param name="is_strand_specific" value="true"/>
1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
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295 <param name="norm" value="false"/>
1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
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296 <param name="library_type" value="RF"/>
1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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297 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
21
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298 <output name="gene_to_trans" file="raw/Trinity.map" compare="sim_size" />
0
1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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299 </test>
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iuc
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300 <test>
21
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301 <param name="pool_mode" value="Yes" />
0
1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
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302 <param name="paired_or_single" value="paired"/>
3
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iuc
parents: 2
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303 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
8ffafd84a7b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 72247137f912b62dd5a3bc566524988bce10b515
iuc
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304 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
0
1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
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305 <param name="is_strand_specific" value="true"/>
1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
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306 <param name="norm" value="true"/>
1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
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307 <param name="library_type" value="RF"/>
1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
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308 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
21
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309 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />
0
1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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310 </test>
18
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311 <test>
21
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312 <param name="pool_mode" value="Yes" />
18
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313 <param name="paired_or_single" value="paired_collection"/>
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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314 <param name="pair_input">
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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315 <collection type="list:paired">
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316 <element name="pair1">
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317 <collection type="paired">
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318 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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319 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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320 </collection>
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321 </element>
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iuc
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322 <element name="pair2">
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323 <collection type="paired">
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iuc
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324 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
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325 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
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326 </collection>
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327 </element>
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328 </collection>
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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329 </param>
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
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330 <param name="is_strand_specific" value="true"/>
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
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331 <param name="norm" value="true"/>
87ab70ffdf1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
iuc
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332 <param name="library_type" value="RF"/>
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333 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
21
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334 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />
18
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335 </test>
0
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336 </tests>
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337 <help>
18
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338 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
0
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339
18
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340 .. _Trinity: http://trinityrnaseq.github.io
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1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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341 </help>
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80c6d1ec9cd7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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342 <expand macro="citation" />
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1d4dd6e51f8c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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343 </tool>