Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix
annotate abundance_estimates_to_matrix.xml @ 21:400691c87530 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
author | iuc |
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date | Tue, 08 Aug 2023 09:13:04 +0000 |
parents | a009c96c5c18 |
children | ba3720d7e68b |
rev | line source |
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a009c96c5c18
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_abundance_estimates_to_matrix" name="Build expression matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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2 <description>for a de novo assembly of RNA-Seq data by Trinity</description> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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3 <macros> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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4 <import>macros.xml</import> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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5 </macros> |
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442e3696c634
"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 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
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7 <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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8 <command detect_errors="aggressive"><![CDATA[ |
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fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
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9 #import re |
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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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10 #for $entry in $samples: |
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8b5039bdf1f6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
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11 ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && |
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77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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12 #end for |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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13 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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14 abundance_estimates_to_matrix.pl |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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15 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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16 --est_method ${est_method} |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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17 --cross_sample_norm ${additional_params.cross_sample_norm} |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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18 |
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13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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19 #if $gene_trans_map: |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
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20 --gene_trans_map '$gene_trans_map' |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
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21 #else: |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
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22 --gene_trans_map 'none' |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
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23 #end if |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
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24 |
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77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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changeset
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25 #for $entry in $samples: |
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fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
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26 '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' |
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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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27 #end for |
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13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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28 |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
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29 && mv *.isoform.counts.matrix '$trans_counts' |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
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30 && mv *.isoform.TPM.not_cross_norm '$TPM_no_norm' |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
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31 #if $gene_trans_map: |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
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32 && mv *.gene.counts.matrix '$trans_counts_gene' |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
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33 && mv *.gene.TPM.not_cross_norm '$TPM_no_norm_gene' |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
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34 #end if |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
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35 |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
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36 #if $additional_params.cross_sample_norm == "TMM": |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
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37 && mv *.isoform.TMM.EXPR.matrix '$norm_TMM' |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
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38 #if $gene_trans_map: |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
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39 && mv *.gene.TMM.EXPR.matrix '$norm_TMM_gene' |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
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40 #end if |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
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41 #else if $additional_params.cross_sample_norm == "UpperQuartile": |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
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42 && mv *.isoform.UpperQuartile.EXPR.matrix '$norm_UQ' |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
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43 #if $gene_trans_map: |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
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44 && mv *.gene.UpperQuartile.EXPR.matrix '$norm_UQ_gene' |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
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45 #end if |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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46 #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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47 ]]></command> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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48 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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49 <param name="samples" type="data" format="tabular" multiple="true" label="Abundance estimates" help="output(s) from 'Align reads and estimate abundance' tool" /> |
a009c96c5c18
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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50 <param argument="--gene_trans_map" type="data" format="tabular" optional="true" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" help="Only needed for gene level estimates" /> |
a009c96c5c18
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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51 <param type="select" argument="--est_method" label="Abundance estimation 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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52 <option value="RSEM">RSEM</option> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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53 <option value="eXpress">eXpress</option> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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54 <option value="salmon">Salmon</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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55 <option value="kallisto">Kallisto</option> |
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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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56 </param> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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57 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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58 <section name="additional_params" title="Additional Options" expanded="False"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
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59 <param type="select" argument="--cross_sample_norm" label="Cross sample normalization"> |
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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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60 <option value="TMM">TMM</option> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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61 <option value="UpperQuartile">UpperQuartile</option> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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62 <option value="none">None</option> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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63 </param> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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64 </section> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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65 </inputs> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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66 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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67 <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment isoform counts (raw counts)"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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68 <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: Matrix of isoform TPM expression values (not cross-sample normalized)"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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69 |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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70 <data format="tabular" name="trans_counts_gene" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment gene counts (raw counts)"> |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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71 <filter>gene_trans_map</filter> |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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72 </data> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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73 <data format="tabular" name="TPM_no_norm_gene" label="${tool.name} on ${on_string}: Matrix of gene TPM expression values (not cross-sample normalized)"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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74 <filter>gene_trans_map</filter> |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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75 </data> |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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76 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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77 <data format="tabular" name="norm_TMM" label="${tool.name} on ${on_string}: Matrix of TMM-normalized expression values"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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78 <filter>additional_params['cross_sample_norm'] == "TMM"</filter> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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79 </data> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
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diff
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80 <data format="tabular" name="norm_UQ" label="${tool.name} on ${on_string}: Matrix of UpperQuartile-normalized expression values"> |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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changeset
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81 <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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changeset
|
82 </data> |
10
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
diff
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|
83 |
20
a009c96c5c18
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents:
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diff
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|
84 <data format="tabular" name="norm_TMM_gene" label="${tool.name} on ${on_string}: Matrix of TMM-normalized expression values (gene)"> |
10
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
diff
changeset
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85 <filter>additional_params['cross_sample_norm'] == "TMM" and gene_trans_map</filter> |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
diff
changeset
|
86 </data> |
20
a009c96c5c18
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
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diff
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|
87 <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: Matrix of UpperQuartile-normalized expression values (gene)"> |
10
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
diff
changeset
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88 <filter>additional_params['cross_sample_norm'] == "UpperQuartile" and gene_trans_map</filter> |
13ab393ba794
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents:
7
diff
changeset
|
89 </data> |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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changeset
|
90 </outputs> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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changeset
|
91 <tests> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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changeset
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92 <test> |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
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0
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93 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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changeset
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94 <param name="est_method" value="RSEM"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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changeset
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95 <param name="cross_sample_norm" value="TMM"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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changeset
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96 <output name="trans_counts"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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97 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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changeset
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98 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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changeset
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99 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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changeset
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100 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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101 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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102 <output name="TPM_no_norm"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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103 <assert_contents> |
77fc547df6ff
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iuc
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104 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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105 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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changeset
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106 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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107 </output> |
10
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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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108 <output name="norm_TMM"> |
0
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iuc
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109 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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110 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
77fc547df6ff
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111 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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112 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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113 </output> |
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iuc
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114 </test> |
77fc547df6ff
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iuc
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115 <test> |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
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116 <param name="samples" ftype="tabular" value="count/rsem_bowtie2/sample_A,count/rsem_bowtie2/sample_B"/> |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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117 <param name="est_method" value="RSEM"/> |
77fc547df6ff
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118 <param name="cross_sample_norm" value="TMM"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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119 <output name="trans_counts"> |
77fc547df6ff
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iuc
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120 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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121 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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122 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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123 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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124 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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125 <output name="TPM_no_norm"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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126 <assert_contents> |
77fc547df6ff
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127 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
77fc547df6ff
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128 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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129 </assert_contents> |
77fc547df6ff
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iuc
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130 </output> |
10
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iuc
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131 <output name="norm_TMM"> |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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132 <assert_contents> |
77fc547df6ff
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133 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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134 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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135 </assert_contents> |
77fc547df6ff
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iuc
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136 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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137 </test> |
77fc547df6ff
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iuc
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138 <test> |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
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0
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139 <param name="samples" ftype="tabular" value="count/express_bowtie/sample_A,count/express_bowtie/sample_B"/> |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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140 <param name="est_method" value="eXpress"/> |
77fc547df6ff
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141 <param name="cross_sample_norm" value="TMM"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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142 <output name="trans_counts"> |
77fc547df6ff
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iuc
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143 <assert_contents> |
77fc547df6ff
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144 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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145 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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146 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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147 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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148 <output name="TPM_no_norm"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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149 <assert_contents> |
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150 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
77fc547df6ff
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151 <has_n_columns n="3" /> |
77fc547df6ff
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152 </assert_contents> |
77fc547df6ff
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153 </output> |
10
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iuc
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154 <output name="norm_TMM"> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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155 <assert_contents> |
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iuc
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156 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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157 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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158 </assert_contents> |
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159 </output> |
77fc547df6ff
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iuc
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160 </test> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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161 <test> |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
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0
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162 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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163 <param name="est_method" value="RSEM"/> |
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164 <param name="cross_sample_norm" value="UpperQuartile"/> |
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165 <output name="trans_counts"> |
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166 <assert_contents> |
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167 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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168 <has_n_columns n="3" /> |
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169 </assert_contents> |
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170 </output> |
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171 <output name="TPM_no_norm"> |
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172 <assert_contents> |
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173 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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174 <has_n_columns n="3" /> |
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175 </assert_contents> |
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176 </output> |
10
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177 <output name="norm_UQ"> |
0
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178 <assert_contents> |
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179 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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180 </assert_contents> |
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181 </output> |
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182 </test> |
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183 <test> |
1
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184 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> |
0
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185 <param name="est_method" value="RSEM"/> |
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186 <param name="cross_sample_norm" value="none"/> |
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187 <output name="trans_counts"> |
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188 <assert_contents> |
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189 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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190 <has_n_columns n="3" /> |
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191 </assert_contents> |
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192 </output> |
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193 <output name="TPM_no_norm"> |
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194 <assert_contents> |
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195 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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196 <has_n_columns n="3" /> |
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197 </assert_contents> |
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198 </output> |
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199 </test> |
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200 <test> |
1
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201 <param name="samples" ftype="tabular" value="count/salmon/sample_A,count/salmon/sample_B"/> |
0
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202 <param name="est_method" value="salmon"/> |
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203 <param name="cross_sample_norm" value="none"/> |
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204 <output name="trans_counts"> |
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205 <assert_contents> |
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206 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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207 <has_n_columns n="3" /> |
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208 </assert_contents> |
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209 </output> |
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210 <output name="TPM_no_norm"> |
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211 <assert_contents> |
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212 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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213 <has_n_columns n="3" /> |
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214 </assert_contents> |
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215 </output> |
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216 </test> |
6
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217 <test> |
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218 <param name="samples" ftype="tabular" value="count/kallisto/abundance.tsv.genes,count/kallisto/abundance_B.tsv.genes"/> |
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219 <param name="est_method" value="kallisto"/> |
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220 <param name="cross_sample_norm" value="TMM"/> |
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221 <output name="trans_counts"> |
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222 <assert_contents> |
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223 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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224 <has_n_columns n="3" /> |
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225 </assert_contents> |
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226 </output> |
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227 <output name="TPM_no_norm"> |
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228 <assert_contents> |
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229 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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230 <has_n_columns n="3" /> |
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231 </assert_contents> |
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232 </output> |
10
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233 <output name="norm_TMM"> |
6
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234 <assert_contents> |
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235 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
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236 <has_n_columns n="3" /> |
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237 </assert_contents> |
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238 </output> |
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239 </test> |
0
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240 </tests> |
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241 <help> |
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242 <![CDATA[ |
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243 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. |
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244 This tool will combine abundance estimations (produced by 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool) from multiple samples into a single tabular file. |
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245 This matrix can then be used by 'RNASeq samples quality check for transcript quantification' and 'Differential Expression Analysis using a Trinity assembly' tools. |
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246 |
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247 **Inputs** |
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248 |
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249 It takes as input multiple results from 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool/ |
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250 Each sample must have a name, that should be used in subsequent tools. |
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251 |
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252 **Output** |
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253 |
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254 This tool will produce a single matrix file. More details on this page: |
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255 |
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256 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification |
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257 |
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258 |
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259 .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki |
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260 ]]> |
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261 </help> |
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262 |
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263 <expand macro="citation" /> |
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264 </tool> |