Mercurial > repos > iuc > trinity_align_and_estimate_abundance
annotate align_and_estimate_abundance.xml @ 10:afd41a430a76 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
author | iuc |
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date | Thu, 14 Jun 2018 03:11:22 -0400 |
parents | 3baf18bcf03e |
children | aed859a021c0 |
rev | line source |
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10
afd41a430a76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@"> |
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a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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2 <description>on a de novo assembly of RNA-Seq data</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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3 <macros> |
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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> |
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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6 <expand macro="requirements"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
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7 <requirement type="package" version="1.3.0">rsem</requirement> |
be3607a306af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
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8 <requirement type="package" version="1.5.1">express</requirement> |
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3baf18bcf03e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 6d3a6d130b58b15190bf286b9840caa162a2bea1
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9 <requirement type="package" version="0.9.1">salmon</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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10 <requirement type="package" version="0.43.1">kallisto</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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11 </expand> |
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be3607a306af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
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12 <command detect_errors="aggressive"><![CDATA[ |
be3607a306af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
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13 ln -f -s '$transcripts' input.fa && |
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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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14 |
10
afd41a430a76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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15 #if $additional_params.gene_map.has_gene_map == "yes": |
afd41a430a76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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16 get_Trinity_gene_to_trans_map.pl input.fa > gene_to_trans.map && |
afd41a430a76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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17 #else: |
afd41a430a76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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18 ln -f -s '$additional_params.gene_map.gene_trans_map' gene_to_trans.map && |
afd41a430a76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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19 #end if |
afd41a430a76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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20 |
0
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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21 #if $inputs.paired_or_single == "paired": |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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22 #if $inputs.left_input.is_of_type('fasta'): |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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23 ln -s '$inputs.left_input' paired_left.fa && |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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24 ln -s '$inputs.right_input' paired_right.fa |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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25 #else: |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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26 ln -s '$inputs.left_input' paired_left.fq && |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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27 ln -s '$inputs.right_input' paired_right.fq |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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28 #end if |
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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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29 #else: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit b9a2194247d728ef4d5a3c5511aa6ea63e9b2bcb
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30 #if $inputs.input.is_of_type('fasta'): |
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a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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31 ln -s '$inputs.input' single.fa |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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32 #else: |
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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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33 ln -s '$inputs.input' single.fq |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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34 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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35 #end if |
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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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36 |
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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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37 && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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38 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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39 align_and_estimate_abundance.pl |
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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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40 |
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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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41 --transcripts input.fa |
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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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42 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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43 --est_method $method.est_method |
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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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44 #if $method.est_method == "RSEM" or $method.est_method == "eXpress": |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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45 --aln_method $method.aln_method |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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46 #else if $method.est_method == "salmon": |
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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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47 --salmon_idx_type $method.salmon_idx_type |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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48 #end if |
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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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49 |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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50 #if $inputs.paired_or_single == "paired": |
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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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51 |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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52 #if $inputs.left_input.is_of_type('fasta'): |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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53 --left paired_left.fa --right paired_right.fa --seqType fa |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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54 #else: |
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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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55 --left paired_left.fq --right paired_right.fq --seqType fq |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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56 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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57 |
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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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58 #if $inputs.strand.is_strand_specific: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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59 --SS_lib_type $inputs.strand.library_type |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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60 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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61 |
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62 --max_ins_size $inputs.paired_fragment_length |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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63 |
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64 #else: |
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65 #if $inputs.input.is_of_type('fasta'): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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66 --single single.fa --seqType fa |
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67 #else: |
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68 --single single.fq --seqType fq |
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69 #end if |
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70 |
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71 #if $inputs.strand.is_strand_specific: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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72 --SS_lib_type $inputs.strand.library_type |
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73 #end if |
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74 #end if |
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75 |
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76 ## Additional parameters. |
10
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77 --gene_trans_map gene_to_trans.map |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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78 |
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79 --prep_reference |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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80 |
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81 --output_dir output |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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82 |
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83 ## CPU |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
84 --thread_count \${GALAXY_SLOTS:-4} |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
85 ]]></command> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
86 <inputs> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
87 <param format="fasta" name="transcripts" argument="--transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
88 <conditional name="inputs"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
89 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
90 <option value="paired">Paired</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
91 <option value="single">Single</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
92 </param> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
93 <when value="paired"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
94 <param format="fasta,fastqsanger" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
95 <param format="fasta,fastqsanger" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
96 <conditional name="strand"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
97 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
98 <when value="false"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
99 </when> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
100 <when value="true"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
101 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
102 <option value="FR">Forward-Reverse</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
103 <option value="RF">Reverse-Forward</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
104 </param> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
105 </when> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
106 </conditional> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
107 <param name="paired_fragment_length" argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
108 </when> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
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109 <when value="single"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
110 <param format="fasta,fastqsanger" argument="--single" name="input" type="data" label="Single-end reads" help=""/> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
111 <conditional name="strand"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
112 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
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113 <when value="false"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
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114 </when> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
115 <when value="true"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
116 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
117 <option value="F">F</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
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118 <option value="R">R</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
119 </param> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
120 </when> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
121 </conditional> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
122 </when> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
123 </conditional> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
124 |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
125 <conditional name="method"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
126 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
127 <option value="RSEM">RSEM</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
128 <option value="eXpress">eXpress</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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changeset
|
129 <option value="salmon">Salmon</option> |
6
04bd98a9c751
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents:
5
diff
changeset
|
130 <option value="kallisto">Kallisto</option> |
0
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
131 </param> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
132 <when value="RSEM"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
133 <param type="select" name="aln_method" argument="--aln_method" label="Alignment method"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
134 <option value="bowtie">Bowtie</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
135 <option value="bowtie2">Bowtie2</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
136 </param> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
137 </when> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
138 <when value="eXpress"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
139 <param type="select" name="aln_method" argument="--aln_method" label="Alignment method"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
140 <option value="bowtie">Bowtie</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
141 <option value="bowtie2">Bowtie2</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
142 </param> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
143 </when> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
144 <when value="salmon"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
145 <param type="select" name="salmon_idx_type" argument="--salmon_idx_type" label="Index type"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
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146 <option value="quasi">Quasi</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
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147 <option value="fmd">FMD</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
148 </param> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
149 </when> |
6
04bd98a9c751
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents:
5
diff
changeset
|
150 <when value="kallisto"> |
04bd98a9c751
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents:
5
diff
changeset
|
151 </when> |
0
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
152 </conditional> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
153 |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
154 <section name="additional_params" title="Additional Options" expanded="False"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
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155 <conditional name="gene_map"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
156 <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
157 <option value="yes">Yes</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
158 <option value="no">No</option> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
159 </param> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
160 <when value="yes"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
161 </when> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
162 <when value="no"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
163 <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" /> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
164 </when> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
165 </conditional> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
166 |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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167 </section> |
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168 </inputs> |
a21e229da9a1
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169 <outputs> |
a21e229da9a1
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170 <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/RSEM.isoforms.results"> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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171 <filter>method['est_method'] == "RSEM"</filter> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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172 </data> |
a21e229da9a1
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173 <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/RSEM.genes.results"> |
a21e229da9a1
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174 <filter>method['est_method'] == "RSEM"</filter> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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175 </data> |
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176 |
a21e229da9a1
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177 <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/results.xprs"> |
a21e229da9a1
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178 <filter>method['est_method'] == "eXpress"</filter> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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179 </data> |
a21e229da9a1
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180 <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/results.xprs.genes"> |
a21e229da9a1
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181 <filter>method['est_method'] == "eXpress"</filter> |
a21e229da9a1
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182 </data> |
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183 |
a21e229da9a1
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184 <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/quant.sf"> |
a21e229da9a1
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185 <filter>method['est_method'] == "salmon"</filter> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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186 </data> |
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187 <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes"> |
a21e229da9a1
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188 <filter>method['est_method'] == "salmon"</filter> |
a21e229da9a1
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189 </data> |
6
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190 |
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191 <data format="tabular" name="isoforms_counts_kallisto" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/abundance.tsv"> |
04bd98a9c751
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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192 <filter>method['est_method'] == "kallisto"</filter> |
04bd98a9c751
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
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193 </data> |
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194 <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/abundance.tsv.genes"> |
04bd98a9c751
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
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195 <filter>method['est_method'] == "kallisto"</filter> |
04bd98a9c751
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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196 </data> |
0
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197 </outputs> |
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198 <tests> |
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199 <test> |
a21e229da9a1
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200 <param name="paired_or_single" value="paired"/> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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201 <param name="left_input" value="reads.left.fq"/> |
a21e229da9a1
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iuc
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202 <param name="right_input" value="reads.right.fq"/> |
a21e229da9a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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203 <param name="transcripts" value="raw/Trinity.fasta"/> |
10
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204 <param name="gene_to_trans" value="raw/Trinity.map" /> |
0
a21e229da9a1
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205 <param name="library_type" value="RF"/> |
a21e229da9a1
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206 <param name="est_method" value="RSEM"/> |
a21e229da9a1
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207 <param name="aln_method" value="bowtie"/> |
a21e229da9a1
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208 <param name="has_gene_map" value="yes"/> |
a21e229da9a1
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209 <output name="isoforms_counts_rsem"> |
a21e229da9a1
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210 <assert_contents> |
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211 <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> |
a21e229da9a1
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212 <has_n_columns n="8" /> |
a21e229da9a1
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213 </assert_contents> |
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214 </output> |
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215 <output name="genes_counts_rsem"> |
a21e229da9a1
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216 <assert_contents> |
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217 <has_line_matching expression="TRINITY_DN0_c0_g1	.*" /> |
a21e229da9a1
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218 <has_n_columns n="7" /> |
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219 </assert_contents> |
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220 </output> |
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221 </test> |
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222 <test> |
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223 <param name="paired_or_single" value="paired"/> |
a21e229da9a1
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224 <param name="left_input" value="reads.left.fq"/> |
a21e229da9a1
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225 <param name="right_input" value="reads.right.fq"/> |
a21e229da9a1
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226 <param name="transcripts" value="raw/Trinity.fasta"/> |
10
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227 <param name="gene_to_trans" value="raw/Trinity.map" /> |
0
a21e229da9a1
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228 <param name="library_type" value="RF"/> |
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229 <param name="est_method" value="RSEM"/> |
a21e229da9a1
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230 <param name="aln_method" value="bowtie2"/> |
a21e229da9a1
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231 <param name="has_gene_map" value="yes"/> |
a21e229da9a1
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iuc
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232 <output name="isoforms_counts_rsem"> |
a21e229da9a1
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233 <assert_contents> |
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234 <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> |
a21e229da9a1
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235 <has_n_columns n="8" /> |
a21e229da9a1
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236 </assert_contents> |
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237 </output> |
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238 <output name="genes_counts_rsem"> |
a21e229da9a1
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239 <assert_contents> |
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240 <has_line_matching expression="TRINITY_DN0_c0_g1	.*" /> |
a21e229da9a1
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241 <has_n_columns n="7" /> |
a21e229da9a1
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242 </assert_contents> |
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243 </output> |
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244 </test> |
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245 <test> |
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246 <param name="paired_or_single" value="paired"/> |
a21e229da9a1
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iuc
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247 <param name="left_input" value="reads.left.fq"/> |
a21e229da9a1
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248 <param name="right_input" value="reads.right.fq"/> |
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249 <param name="transcripts" value="raw/Trinity.fasta"/> |
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250 <param name="gene_to_trans" value="raw/Trinity.map" /> |
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251 <param name="library_type" value="RF"/> |
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252 <param name="est_method" value="eXpress"/> |
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253 <param name="aln_method" value="bowtie"/> |
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254 <param name="has_gene_map" value="yes"/> |
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255 <output name="isoforms_counts_express"> |
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256 <assert_contents> |
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257 <has_line_matching expression=".*	TRINITY_DN2_c3_g1_i1	.*" /> |
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258 <has_n_columns n="15" /> |
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259 </assert_contents> |
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260 </output> |
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261 <output name="genes_counts_express"> |
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262 <assert_contents> |
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263 <has_line_matching expression="NA	TRINITY_DN3_c0_g1.*" /> |
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264 <has_n_columns n="15" /> |
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265 </assert_contents> |
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266 </output> |
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267 </test> |
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268 <test> |
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269 <param name="paired_or_single" value="paired"/> |
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270 <param name="left_input" value="reads.left.fq"/> |
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271 <param name="right_input" value="reads.right.fq"/> |
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272 <param name="transcripts" value="raw/Trinity.fasta"/> |
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273 <param name="gene_to_trans" value="raw/Trinity.map" /> |
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274 <param name="library_type" value="RF"/> |
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275 <param name="est_method" value="salmon"/> |
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276 <param name="aln_method" value="bowtie"/> |
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277 <param name="has_gene_map" value="yes"/> |
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278 <output name="isoforms_counts_salmon"> |
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279 <assert_contents> |
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280 <has_line_matching expression="TRINITY_DN2_c3_g1_i1	.*" /> |
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281 <has_n_columns n="5" /> |
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282 </assert_contents> |
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283 </output> |
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284 <output name="genes_counts_salmon"> |
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285 <assert_contents> |
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286 <has_line_matching expression="TRINITY_DN3_c0_g1.*" /> |
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287 <has_n_columns n="5" /> |
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288 </assert_contents> |
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289 </output> |
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290 </test> |
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291 <test> |
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292 <param name="paired_or_single" value="paired"/> |
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293 <param name="left_input" value="reads.left.fq"/> |
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294 <param name="right_input" value="reads.right.fq"/> |
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295 <param name="transcripts" value="raw/Trinity.fasta"/> |
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296 <param name="gene_to_trans" value="raw/Trinity.map" /> |
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297 <param name="library_type" value="RF"/> |
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298 <param name="est_method" value="kallisto"/> |
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299 <param name="has_gene_map" value="yes"/> |
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300 <output name="isoforms_counts_kallisto"> |
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301 <assert_contents> |
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302 <has_line_matching expression="TRINITY_DN1_c0_g1_i1	.*" /> |
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303 <has_n_columns n="5" /> |
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304 </assert_contents> |
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305 </output> |
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306 <output name="genes_counts_kallisto"> |
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307 <assert_contents> |
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308 <has_line_matching expression="TRINITY_DN1_c0_g1	.*" /> |
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309 <has_n_columns n="5" /> |
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310 </assert_contents> |
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311 </output> |
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312 </test> |
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313 </tests> |
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314 <help> |
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315 <![CDATA[ |
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316 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. |
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317 This tool estimates the abundance of isoforms and genes of a transcriptome assembled with Trinity, using FastQ of a specific sample. |
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318 |
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319 **Inputs** |
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320 |
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321 It takes as input a transcriptome assembled with Trinity and the reads from a RNASeq sample. |
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322 You have to choose between several counting methods. |
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323 |
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324 If you dont align on a Trinity assembly, you need to provide a file of the following (tabular) format to map gene ids to transcript ids: |
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325 |
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326 =========== ================ |
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327 gene1 transcript1 |
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328 ----------- ---------------- |
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329 gene2 transcript2 |
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330 =========== ================ |
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331 |
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332 **Output** |
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333 |
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334 This tool will produce 2 tabular files, with counts for isoforms and genes respectively. More details on this page: |
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335 |
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336 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification |
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337 |
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338 |
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339 .. _Trinity: http://trinityrnaseq.github.io |
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340 ]]> |
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341 </help> |
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342 |
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343 <expand macro="citation" /> |
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344 </tool> |