Mercurial > repos > iuc > trinity
annotate trinity.xml @ 21:ca0588b09438 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 482fb46ba8d588f2294e21829a0904809b0ec3f1
author | iuc |
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date | Thu, 23 Aug 2018 12:54:35 -0400 |
parents | 171b827eadf2 |
children | c9cfec002f71 |
rev | line source |
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20
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@"> |
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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> |
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831abd20e690
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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3 <macros> |
831abd20e690
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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4 <import>macros.xml</import> |
831abd20e690
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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5 </macros> |
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e65e640e6196
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
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6 <expand macro="requirements" /> |
e65e640e6196
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
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7 <command detect_errors="aggressive"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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8 if [ -z "\$GALAXY_MEMORY_MB" ] ; then |
cee61b3fcf78
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 ; |
cee61b3fcf78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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10 else |
cee61b3fcf78
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)) ; |
cee61b3fcf78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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12 fi ; |
cee61b3fcf78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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13 |
cee61b3fcf78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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14 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then |
cee61b3fcf78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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15 workdir=`pwd` ; |
cee61b3fcf78
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" ; |
cee61b3fcf78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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17 fi ; |
cee61b3fcf78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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18 |
18
d3b1249af60c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
iuc
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19 #if $additional_params.guided.is_guided == "yes": |
d3b1249af60c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
iuc
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20 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' && |
d3b1249af60c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
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21 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' && |
d3b1249af60c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
iuc
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22 #end if |
d3b1249af60c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
iuc
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23 Trinity --no_version_check |
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606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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24 |
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171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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25 ## Inputs |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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26 #if $pool.pool_mode == "Yes": |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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27 #if str($pool.inputs.paired_or_single) == "single": |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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28 --single ${ ','.join(['"%s"' % x for x in $pool.inputs.input]) } |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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29 #if $pool.inputs.input[0].is_of_type('fasta'): |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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30 --seqType fa |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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31 #else: |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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32 --seqType fq |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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33 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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34 |
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171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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35 #if $pool.inputs.strand.is_strand_specific: |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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36 --SS_lib_type $pool.inputs.strand.library_type |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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37 #end if |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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38 #elif str($pool.inputs.paired_or_single) == "paired": |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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39 --left ${ ','.join(['"%s"' % x for x in $pool.inputs.left_input]) } |
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c7555bc21812
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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40 |
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171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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41 --right ${ ','.join(['"%s"' % x for x in $pool.inputs.right_input]) } |
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199aa6821ca5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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42 |
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171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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43 #if $pool.inputs.left_input[0].is_of_type('fasta'): |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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44 --seqType fa |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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45 #else: |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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46 --seqType fq |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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47 #end if |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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48 @COMMAND_PAIRED_STRAND_JACCARD@ |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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49 #elif str($pool.inputs.paired_or_single) == "paired_collection": |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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50 --left ${ ','.join(['"%s"' % x.forward for x in $pool.inputs.pair_input]) } |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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51 --right ${ ','.join(['"%s"' % x.reverse for x in $pool.inputs.pair_input]) } |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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52 #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'): |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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53 --seqType fa |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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54 #else: |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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55 --seqType fq |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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56 #end if |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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57 @COMMAND_PAIRED_STRAND_JACCARD@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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58 #end if |
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171b827eadf2
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59 #elif $pool.pool_mode == "No": |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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60 #if $pool.inputs.paired_or_single == "unmerged_paired_collection": |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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61 --left $pool.inputs.pair_input.forward |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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62 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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63 --right $pool.inputs.pair_input.reverse |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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64 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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65 #if $pool.inputs.pair_input.forward.is_of_type('fasta'): |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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66 --seqType fa |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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67 #else: |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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68 --seqType fq |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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69 #end if |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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70 @COMMAND_PAIRED_STRAND_JACCARD@ |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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71 #elif $pool.inputs.paired_or_single == "unmerged_single_collection": |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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72 --single $pool.inputs.input |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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73 |
20
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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74 #if $pool.inputs.input.is_of_type('fasta'): |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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75 --seqType fa |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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76 #else: |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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77 --seqType fq |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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78 #end if |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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79 |
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80 #if $pool.inputs.strand.is_strand_specific: |
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81 --SS_lib_type $pool.inputs.strand.library_type |
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82 #end if |
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83 #end if |
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84 #end if |
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85 $norm |
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86 |
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87 ## Additional parameters. |
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88 #if $additional_params.min_contig_length: |
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89 --min_contig_length $additional_params.min_contig_length |
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90 #end if |
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91 #if $additional_params.long_reads: |
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92 --long_reads $additional_params.long_reads |
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93 #end if |
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94 #if $additional_params.guided.is_guided == "yes": |
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95 --genome_guided_bam 'localbam.bam' |
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96 |
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97 #if $additional_params.guided.genome_guided_min_coverage: |
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98 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage |
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99 #end if |
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100 |
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101 #if $additional_params.guided.genome_guided_min_reads_per_partition: |
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102 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition |
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103 #end if |
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104 |
18
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105 #if $additional_params.guided.genome_guided_max_intron: |
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106 --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron |
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107 #end if |
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108 #end if |
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109 |
10
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110 #if $additional_params.min_kmer_cov: |
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111 --min_kmer_cov $additional_params.min_kmer_cov |
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112 #end if |
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113 |
0
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114 ## CPU and butterfly options. |
19
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115 --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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116 |
2
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117 ## > $trinity_log 2>&1 |
19
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118 |
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119 && |
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120 |
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121 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then |
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122 mkdir -p "\$workdir/trinity_out_dir"; |
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123 cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir"; |
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124 cd "\$workdir"; |
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125 fi ; |
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126 |
0
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127 ]]></command> |
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128 <inputs> |
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129 <conditional name="pool"> |
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130 <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" > |
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131 <option value="No">No</option> |
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132 <option value="Yes" selected="True">Yes</option> |
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133 </param> |
20
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134 <when value="Yes" > |
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135 <conditional name="inputs"> |
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136 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> |
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137 <option value="single" selected="true">Single-end</option> |
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138 <option value="paired">Paired-end</option> |
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139 <option value="paired_collection">Paired-end collection</option> |
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140 </param> |
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141 <when value="single"> |
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142 <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/> |
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143 <conditional name="strand"> |
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144 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> |
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145 <when value="false"> |
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146 </when> |
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147 <when value="true"> |
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148 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> |
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149 <option value="F">F</option> |
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150 <option value="R">R</option> |
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151 </param> |
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152 </when> |
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153 </conditional> |
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154 </when> |
20
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155 <when value="paired"> |
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156 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" /> |
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157 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" /> |
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158 <expand macro="input_paired_strand_jaccard" /> |
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159 </when> |
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160 <when value="paired_collection"> |
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161 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/> |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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162 <expand macro="input_paired_strand_jaccard" /> |
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163 </when> |
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164 </conditional> |
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165 </when> |
20
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166 <when value="No"> |
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167 <conditional name="inputs"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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168 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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169 <option value="unmerged_single_collection">Single-end</option> |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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170 <option value="unmerged_paired_collection">Paired-end</option> |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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171 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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172 <when value="unmerged_single_collection"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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173 <param name="input" argument="--single" type="data" format="fasta,fastqsanger" label="Single-end reads" help="Elements of collection will NOT be merged"/> |
171b827eadf2
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174 <conditional name="strand"> |
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175 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> |
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176 <when value="false"> |
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177 </when> |
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178 <when value="true"> |
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179 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> |
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180 <option value="F">F</option> |
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181 <option value="R">R</option> |
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182 </param> |
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183 </when> |
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184 </conditional> |
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185 </when> |
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186 <when value="unmerged_paired_collection"> |
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187 <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/> |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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188 <expand macro="input_paired_strand_jaccard" /> |
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189 </when> |
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190 </conditional> |
17
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191 </when> |
0
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192 </conditional> |
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193 <param name="norm" type="boolean" argument="--normalize_reads" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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194 <section name="additional_params" title="Additional Options" expanded="False"> |
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195 <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"/> |
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196 |
0
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197 <conditional name="guided"> |
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198 <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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199 <option value="no">No</option> |
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200 <option value="yes">Yes</option> |
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201 </param> |
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202 <when value="no"> |
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203 </when> |
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204 <when value="yes"> |
18
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205 <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" /> |
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206 <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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207 <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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208 <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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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209 </when> |
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210 </conditional> |
3
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211 |
17
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212 <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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213 |
10
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214 <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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215 </section> |
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216 </inputs> |
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217 <outputs> |
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218 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> |
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219 <data name="gene_to_trans" format="tabular" label="${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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220 </outputs> |
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221 <tests> |
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222 <test> |
20
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223 <param name="pool_mode" value="No" /> |
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224 <param name="paired_or_single" value="unmerged_paired_collection"/> |
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225 <param name="pair_input"> |
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226 <collection type="paired"> |
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227 <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> |
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228 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/> |
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229 </collection> |
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230 </param> |
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231 <param name="is_strand_specific" value="true"/> |
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232 <param name="norm" value="true"/> |
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233 <param name="library_type" value="RF"/> |
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234 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" /> |
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235 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" /> |
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236 </test> |
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237 <test> |
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238 <param name="pool_mode" value="No" /> |
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239 <param name="paired_or_single" value="unmerged_single_collection"/> |
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240 <param name="input" value="reads.left.fq" ftype="fastqsanger"/> |
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241 <param name="is_strand_specific" value="true"/> |
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242 <param name="norm" value="false"/> |
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243 <param name="library_type" value="F"/> |
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244 <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" /> |
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245 <output name="gene_to_trans" file="raw/Trinity_single_unmerged_1.map" compare="sim_size" /> |
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246 </test> |
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247 <test> |
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248 <param name="pool_mode" value="Yes" /> |
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249 <param name="paired_or_single" value="paired"/> |
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250 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> |
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251 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> |
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252 <param name="is_strand_specific" value="true"/> |
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253 <param name="norm" value="false"/> |
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254 <param name="library_type" value="RF"/> |
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255 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" /> |
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256 <output name="gene_to_trans" file="raw/Trinity.map" compare="sim_size" /> |
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257 </test> |
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258 <test> |
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259 <param name="pool_mode" value="Yes" /> |
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260 <param name="paired_or_single" value="paired"/> |
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261 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> |
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262 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> |
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263 <param name="is_strand_specific" value="true"/> |
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264 <param name="norm" value="true"/> |
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265 <param name="library_type" value="RF"/> |
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266 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> |
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267 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" /> |
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268 </test> |
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269 <test> |
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270 <param name="pool_mode" value="Yes" /> |
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271 <param name="paired_or_single" value="paired_collection"/> |
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272 <param name="pair_input"> |
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273 <collection type="list:paired"> |
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274 <element name="pair1"> |
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275 <collection type="paired"> |
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276 <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> |
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277 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/> |
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278 </collection> |
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279 </element> |
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280 <element name="pair2"> |
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281 <collection type="paired"> |
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282 <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> |
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283 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/> |
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284 </collection> |
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285 </element> |
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286 </collection> |
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287 </param> |
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288 <param name="is_strand_specific" value="true"/> |
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289 <param name="norm" value="true"/> |
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290 <param name="library_type" value="RF"/> |
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291 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> |
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292 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" /> |
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293 </test> |
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294 </tests> |
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295 <help> |
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296 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. |
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297 |
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298 .. _Trinity: http://trinityrnaseq.github.io |
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299 </help> |
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300 <expand macro="citation" /> |
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301 </tool> |