Mercurial > repos > iuc > trinity
annotate trinity.xml @ 32:77cf519a812e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
author | iuc |
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date | Tue, 11 Apr 2023 19:57:45 +0000 |
parents | 3772d9a10f27 |
children | 9fa24d5aac68 |
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32
77cf519a812e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
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1 <tool id="trinity" name="Trinity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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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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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
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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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3772d9a10f27
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c468d2b9613f88cc5f96f77ab1e0592d3c9ce707"
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6 <expand macro="bio_tools"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9f23ced8d1f5a7ddf96e5f6cb608f3de8fc76250"
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7 <expand macro="requirements"> |
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77cf519a812e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
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8 <requirement type="package" version="3.2.7">rsync</requirement> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9f23ced8d1f5a7ddf96e5f6cb608f3de8fc76250"
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9 </expand> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
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10 <command detect_errors="aggressive"><![CDATA[ |
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cee61b3fcf78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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11 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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12 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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13 else |
cee61b3fcf78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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14 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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15 fi ; |
cee61b3fcf78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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16 |
cee61b3fcf78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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17 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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18 workdir=`pwd` ; |
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d5e8807a407d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9f23ced8d1f5a7ddf96e5f6cb608f3de8fc76250"
iuc
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19 scratchfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR"); |
d5e8807a407d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9f23ced8d1f5a7ddf96e5f6cb608f3de8fc76250"
iuc
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20 emptyfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR"); |
d5e8807a407d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9f23ced8d1f5a7ddf96e5f6cb608f3de8fc76250"
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21 cd "\$scratchfolder" ; |
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cee61b3fcf78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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22 fi ; |
cee61b3fcf78
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
iuc
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23 |
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d3b1249af60c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
iuc
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24 #if $additional_params.guided.is_guided == "yes": |
d3b1249af60c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
iuc
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25 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' && |
d3b1249af60c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
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26 ln -s '${$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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27 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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28 #if $pool.pool_mode == "Yes": |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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29 #if str($pool.inputs.paired_or_single) == "single": |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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30 #for i, f in enumerate($pool.inputs.input): |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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31 ln -s '$f' input${i}.${f.ext} && |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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32 #end for |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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33 #elif str($pool.inputs.paired_or_single) == "paired": |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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34 #for i, f in enumerate($pool.inputs.left_input): |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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35 ln -s '$f' left_input${i}.${f.ext} && |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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36 #end for |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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37 #for i, f in enumerate($pool.inputs.right_input): |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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38 ln -s '$f' right_input${i}.${f.ext} && |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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39 #end for |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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40 #elif str($pool.inputs.paired_or_single) == "paired_collection": |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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41 #for i, f in enumerate($pool.inputs.pair_input): |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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42 ln -s '$f.forward' 'left_input${i}.${f.forward.ext}' && |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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43 ln -s '$f.reverse' 'right_input${i}.${f.reverse.ext}' && |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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44 #end for |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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45 #end if |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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46 #elif $pool.pool_mode == "No": |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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47 #if $pool.inputs.paired_or_single == "unmerged_paired_collection": |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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48 ln -s '$pool.inputs.pair_input.forward' 'left_input.${$pool.inputs.pair_input.forward.ext}' && |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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49 ln -s '$pool.inputs.pair_input.reverse' 'right_input.${pool.inputs.pair_input.reverse.ext}' && |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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50 #elif $pool.inputs.paired_or_single == "unmerged_single_collection": |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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51 ln -s '$pool.inputs.input' 'input.${pool.inputs.input.ext}' && |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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52 #end if |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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53 #end if |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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54 |
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55 Trinity --no_version_check |
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56 --output ./trinity_out_dir |
77cf519a812e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
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57 ## do not try to run the high-mem normalization stats generator in parallel for paired-end fastqs |
77cf519a812e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
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58 --no_parallel_norm_stats |
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59 ## Inputs |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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60 #if $pool.pool_mode == "Yes": |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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61 #if str($pool.inputs.paired_or_single) == "single": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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62 --single ${ ','.join(["'input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.input)]) } |
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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 #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
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64 --seqType fa |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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65 #else: |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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66 --seqType fq |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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67 #end if |
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68 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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69 #if $pool.inputs.strand.is_strand_specific == 'true': |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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70 --SS_lib_type $pool.inputs.strand.library_type |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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71 #end if |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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72 #elif str($pool.inputs.paired_or_single) == "paired": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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73 --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.left_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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74 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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75 --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.right_input)]) } |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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76 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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77 #if $pool.inputs.left_input[0].is_of_type('fasta'): |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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78 --seqType fa |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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79 #else: |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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80 --seqType fq |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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81 #end if |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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82 @COMMAND_PAIRED_STRAND_JACCARD@ |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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83 #elif str($pool.inputs.paired_or_single) == "paired_collection": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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84 --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.forward.ext) for i, f in enumerate($pool.inputs.pair_input)]) } |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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85 --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.reverse.ext) for i, f in enumerate($pool.inputs.pair_input)]) } |
20
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iuc
parents:
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86 #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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87 --seqType fa |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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88 #else: |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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89 --seqType fq |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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90 #end if |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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91 @COMMAND_PAIRED_STRAND_JACCARD@ |
0
606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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92 #end if |
20
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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93 #elif $pool.pool_mode == "No": |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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94 #if $pool.inputs.paired_or_single == "unmerged_paired_collection": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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95 --left 'left_input.${$pool.inputs.pair_input.forward.ext}' |
0
606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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96 |
27
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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97 --right 'right_input.${pool.inputs.pair_input.reverse.ext}' |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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98 |
20
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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99 #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
iuc
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100 --seqType fa |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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101 #else: |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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102 --seqType fq |
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iuc
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103 #end if |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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104 @COMMAND_PAIRED_STRAND_JACCARD@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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105 #elif $pool.inputs.paired_or_single == "unmerged_single_collection": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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106 --single 'input.${pool.inputs.input.ext}' |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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107 |
27
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
iuc
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108 #if $pool.inputs.input.is_of_type('fasta'): |
20
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109 --seqType fa |
171b827eadf2
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110 #else: |
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iuc
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111 --seqType fq |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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112 #end if |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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113 |
32
77cf519a812e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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114 #if $pool.inputs.strand.is_strand_specific == 'true': |
20
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iuc
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115 --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
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116 #end if |
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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117 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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118 #end if |
32
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119 $no_normalize_reads |
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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120 |
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121 ## Additional parameters. |
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122 #if $additional_params.min_contig_length: |
606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
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123 --min_contig_length $additional_params.min_contig_length |
606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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124 #end if |
606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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125 #if $additional_params.long_reads: |
606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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126 --long_reads $additional_params.long_reads |
606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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127 #end if |
1
0067c78f49dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1abd7a1cbd25b687267df2ebc4dfba5894797a64
iuc
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128 #if $additional_params.guided.is_guided == "yes": |
18
d3b1249af60c
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129 --genome_guided_bam 'localbam.bam' |
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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130 |
606b7748965d
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131 #if $additional_params.guided.genome_guided_min_coverage: |
606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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132 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage |
606b7748965d
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133 #end if |
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134 |
606b7748965d
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135 #if $additional_params.guided.genome_guided_min_reads_per_partition: |
606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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136 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition |
606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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137 #end if |
3
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138 |
18
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139 #if $additional_params.guided.genome_guided_max_intron: |
d3b1249af60c
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140 --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron |
d3b1249af60c
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141 #end if |
0
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142 #end if |
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143 |
10
831abd20e690
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144 #if $additional_params.min_kmer_cov: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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145 --min_kmer_cov $additional_params.min_kmer_cov |
831abd20e690
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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146 #end if |
831abd20e690
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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147 |
0
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148 ## CPU and butterfly options. |
19
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149 --CPU \${GALAXY_SLOTS:-4} --max_memory \${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax \${GALAXY_MEMORY_GB:-1}G --bfly_opts '-V 10 --stderr' |
3
c7555bc21812
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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150 |
2
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151 ## > $trinity_log 2>&1 |
19
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152 |
cee61b3fcf78
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153 && |
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154 |
29
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9f23ced8d1f5a7ddf96e5f6cb608f3de8fc76250"
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155 ## Trinity can create millions of files in the same directory, so the cleaning task makes use of rsync |
d5e8807a407d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9f23ced8d1f5a7ddf96e5f6cb608f3de8fc76250"
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156 ## for ensuring better performances. |
d5e8807a407d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9f23ced8d1f5a7ddf96e5f6cb608f3de8fc76250"
iuc
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157 ## see: https://web.archive.org/web/20130929001850/http://linuxnote.net/jianingy/en/linux/a-fast-way-to-remove-huge-number-of-files.html |
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158 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then |
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159 mkdir -p "\$workdir/trinity_out_dir"; |
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160 cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir"; |
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161 cd "\$TRINITY_SCRATCH_DIR"; |
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162 rsync -a --delete "\$emptyfolder/" "\$scratchfolder/"; |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9f23ced8d1f5a7ddf96e5f6cb608f3de8fc76250"
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163 rmdir "\$emptyfolder" "\$scratchfolder/"; |
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164 cd "\$workdir"; |
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165 fi ; |
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166 |
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167 ]]></command> |
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168 <inputs> |
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169 <conditional name="pool"> |
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170 <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" > |
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171 <option value="No">No</option> |
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172 <option value="Yes" selected="True">Yes</option> |
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173 </param> |
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174 <when value="Yes" > |
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175 <conditional name="inputs"> |
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176 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> |
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177 <option value="single" selected="true">Single-end</option> |
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178 <option value="paired">Paired-end</option> |
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179 <option value="paired_collection">Paired-end collection</option> |
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180 </param> |
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181 <when value="single"> |
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182 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Single-end reads" help=""/> |
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183 <expand macro="is_strand_specific_f_r"/> |
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184 </when> |
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185 <when value="paired"> |
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186 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Left/Forward strand reads" /> |
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187 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Right/Reverse strand reads" /> |
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188 <expand macro="input_paired_strand_jaccard" /> |
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189 </when> |
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190 <when value="paired_collection"> |
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191 <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"/> |
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192 <expand macro="input_paired_strand_jaccard" /> |
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193 </when> |
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194 </conditional> |
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195 </when> |
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196 <when value="No"> |
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197 <conditional name="inputs"> |
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198 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> |
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199 <option value="unmerged_single_collection">Single-end</option> |
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200 <option value="unmerged_paired_collection">Paired-end</option> |
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201 </param> |
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202 <when value="unmerged_single_collection"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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203 <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Single-end reads" help="Elements of collection will NOT be merged"/> |
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204 <expand macro="is_strand_specific_f_r"/> |
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205 </when> |
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206 <when value="unmerged_paired_collection"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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207 <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"/> |
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208 <expand macro="input_paired_strand_jaccard" /> |
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209 </when> |
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210 </conditional> |
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211 </when> |
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212 </conditional> |
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213 <param argument="--no_normalize_reads" type="boolean" truevalue="" falsevalue="--no_normalize_reads" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/> |
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214 <section name="additional_params" title="Additional Options" expanded="False"> |
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215 <param 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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216 |
0
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217 <conditional name="guided"> |
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218 <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"> |
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219 <option value="no">No</option> |
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220 <option value="yes">Yes</option> |
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221 </param> |
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222 <when value="no"> |
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223 </when> |
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224 <when value="yes"> |
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225 <param argument="--genome_guided_bam" type="data" format="bam" label="Coordinate-sorted BAM file" /> |
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226 <param 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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227 <param 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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228 <param 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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229 </when> |
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230 </conditional> |
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231 |
32
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232 <param argument="--long_reads" type="data" format="fasta" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" |
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233 help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/> |
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234 <param argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/> |
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235 </section> |
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236 </inputs> |
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237 <outputs> |
32
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238 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir.Trinity.fasta"/> |
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239 <data name="gene_to_trans" format="tabular" label="${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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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240 </outputs> |
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241 <tests> |
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242 <test> |
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243 <param name="pool_mode" value="No" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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244 <param name="paired_or_single" value="unmerged_paired_collection"/> |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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245 <param name="pair_input"> |
171b827eadf2
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246 <collection type="paired"> |
26
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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247 <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> |
26d5493b20b6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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248 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/> |
26d5493b20b6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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249 </collection> |
26d5493b20b6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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250 </param> |
26d5493b20b6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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251 <param name="is_strand_specific" value="true"/> |
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252 <param name="no_normalize_reads" value="true"/> |
26
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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253 <param name="library_type" value="RF"/> |
26d5493b20b6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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254 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" /> |
26d5493b20b6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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255 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" /> |
26d5493b20b6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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256 </test> |
26d5493b20b6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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257 <test> |
26d5493b20b6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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258 <param name="pool_mode" value="No" /> |
26d5493b20b6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
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259 <param name="paired_or_single" value="unmerged_paired_collection"/> |
26d5493b20b6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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260 <param name="pair_input"> |
26d5493b20b6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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261 <collection type="paired"> |
27
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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262 <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger.gz" /> |
5b60313a6ce7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
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263 <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger.gz" /> |
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264 </collection> |
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265 </param> |
171b827eadf2
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266 <param name="is_strand_specific" value="true"/> |
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267 <param name="no_normalize_reads" value="true"/> |
20
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268 <param name="library_type" value="RF"/> |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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269 <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" /> |
171b827eadf2
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270 <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" /> |
171b827eadf2
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271 </test> |
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272 <test> |
171b827eadf2
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273 <param name="pool_mode" value="No" /> |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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274 <param name="paired_or_single" value="unmerged_single_collection"/> |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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275 <param name="input" value="reads.left.fq" ftype="fastqsanger"/> |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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276 <param name="is_strand_specific" value="true"/> |
32
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277 <param name="no_normalize_reads" value="false"/> |
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278 <param name="library_type" value="F"/> |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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279 <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" /> |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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280 <output name="gene_to_trans" file="raw/Trinity_single_unmerged_1.map" compare="sim_size" /> |
171b827eadf2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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281 </test> |
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282 <test> |
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283 <param name="pool_mode" value="Yes" /> |
0
606b7748965d
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284 <param name="paired_or_single" value="paired"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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285 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> |
c7555bc21812
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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286 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> |
0
606b7748965d
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287 <param name="is_strand_specific" value="true"/> |
32
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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288 <param name="no_normalize_reads" value="false"/> |
0
606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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289 <param name="library_type" value="RF"/> |
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290 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" /> |
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291 <output name="gene_to_trans" file="raw/Trinity.map" compare="sim_size" /> |
0
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292 </test> |
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293 <test> |
20
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294 <param name="pool_mode" value="Yes" /> |
0
606b7748965d
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295 <param name="paired_or_single" value="paired"/> |
3
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296 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> |
c7555bc21812
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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297 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> |
0
606b7748965d
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298 <param name="is_strand_specific" value="true"/> |
32
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299 <param name="no_normalize_reads" value="true"/> |
0
606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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300 <param name="library_type" value="RF"/> |
606b7748965d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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301 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> |
20
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302 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" /> |
0
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303 </test> |
17
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304 <test> |
20
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305 <param name="pool_mode" value="Yes" /> |
17
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306 <param name="paired_or_single" value="paired_collection"/> |
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307 <param name="pair_input"> |
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308 <collection type="list:paired"> |
199aa6821ca5
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309 <element name="pair1"> |
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310 <collection type="paired"> |
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311 <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> |
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312 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/> |
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313 </collection> |
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314 </element> |
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315 <element name="pair2"> |
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316 <collection type="paired"> |
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317 <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> |
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318 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/> |
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319 </collection> |
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320 </element> |
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321 </collection> |
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322 </param> |
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323 <param name="is_strand_specific" value="true"/> |
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324 <param name="no_normalize_reads" value="true"/> |
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325 <param name="library_type" value="RF"/> |
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326 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> |
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327 <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" /> |
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328 </test> |
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329 </tests> |
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330 <help> |
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331 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. |
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332 |
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333 .. _Trinity: http://trinityrnaseq.github.io |
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334 </help> |
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335 <expand macro="citation" /> |
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336 </tool> |