Mercurial > repos > iuc > trinity_filter_low_expr_transcripts
annotate filter_low_expr_transcripts.xml @ 4:e34706d4e786 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
author | iuc |
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date | Thu, 23 Mar 2017 10:16:35 -0400 |
parents | 7246eeaad26d |
children | 30d6a6424102 |
rev | line source |
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1
7246eeaad26d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
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1 <tool id="trinity_filter_low_expr_transcripts" name="Filter low expression transcripts" version="@WRAPPER_VERSION@.1"> |
0
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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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2 <description>from a Trinity assembly</description> |
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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 e23a8ad798830209db722d5496d19ec7a5e06214
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7 <expand macro="stdio"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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8 <command><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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9 filter_low_expr_transcripts.pl |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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10 --matrix "$matrix" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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11 --transcripts "$assembly" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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12 |
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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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13 #if $additional_params.gene_map.has_gene_map == "no": |
1
7246eeaad26d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
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14 --gene_to_trans_map "$additional_params.gene_map.gene_trans_map" |
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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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15 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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16 --trinity_mode |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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17 #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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18 |
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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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19 #if str($min_expr_any): |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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20 --min_expr_any $min_expr_any |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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21 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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22 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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23 #if str($isoform_filter.highest_iso_only) == "yes": |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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24 --highest_iso_only |
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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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25 #else if str($isoform_filter.min_pct_dom_iso): |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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26 --min_pct_dom_iso $isoform_filter.min_pct_dom_iso |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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27 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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28 |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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29 > "$filtered" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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30 ]]></command> |
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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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31 <inputs> |
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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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32 <param format="fasta" name="assembly" argument="--transcripts" type="data" label="Trinity assembly"/> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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33 <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix"/> |
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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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34 |
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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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35 <param name="min_expr_any" type="float" argument="--min_expr_any" optional="true" label="Minimum expression level required across any sample"/> |
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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 |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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37 |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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38 <conditional name="isoform_filter"> |
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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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39 <param name="highest_iso_only" argument="--highest_iso_only" type="select" label="Only retain the most highly expressed isoform per gene"> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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40 <option value="yes">Yes</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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41 <option value="no" selected="true">No</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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42 </param> |
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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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43 <when value="yes"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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44 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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45 <when value="no"> |
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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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46 <param name="min_pct_dom_iso" argument="--min_pct_dom_iso" type="integer" optional="true" label="Minimum percent of dominant isoform expression"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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47 </when> |
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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 </conditional> |
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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 |
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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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50 <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 e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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51 <conditional name="gene_map"> |
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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 <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed"> |
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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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53 <option value="yes">Yes</option> |
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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 <option value="no">No</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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55 </param> |
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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 <when value="yes"> |
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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 </when> |
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58 <when value="no"> |
1
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59 <param format="tabular" name="gene_trans_map" argument="--gene_to_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" /> |
0
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60 </when> |
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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 </conditional> |
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62 |
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63 </section> |
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64 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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65 <outputs> |
4
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66 <data format="fasta" name="filtered" label="${tool.name} on ${on_string}: filtered low expression transcripts"/> |
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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67 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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68 <tests> |
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69 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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70 <param name="matrix" value="filtered/counts.matrix"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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71 <param name="assembly" value="raw/Trinity.fasta" ftype="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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72 <param name="min_expr_any" value="25"/> |
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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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73 <output name="filtered" file="filtered/Trinity_filtered_exp.fasta" /> |
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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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74 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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75 <!-- this option is broken in 2.2.0: https://github.com/trinityrnaseq/trinityrnaseq/issues/129 |
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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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76 <test> |
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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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77 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> |
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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 <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/> |
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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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79 <param name="isoform_filter|highest_iso_only" value="yes"/> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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80 <output name="filtered" file="filtered/Trinity_filtered_hi_iso.fasta" /> |
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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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81 </test--> |
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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 <test> |
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83 <param name="matrix" value="filtered/counts.matrix"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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84 <param name="assembly" value="raw/Trinity.fasta" ftype="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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85 <param name="isoform_filter|min_pct_dom_iso" value="20"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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86 <output name="filtered" file="filtered/Trinity_filtered_pct_iso.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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87 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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88 </tests> |
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89 <help> |
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90 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. |
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91 This tool filters a Trinity assembly using an expression matrix built |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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92 with "Build expression matrix for a de novo assembly of RNA-Seq data by Trinity" tool. |
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93 It discards transcripts/isoforms having a low expression level. |
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94 |
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95 .. _Trinity: http://trinityrnaseq.github.io |
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96 </help> |
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97 |
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98 <expand macro="citation" /> |
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99 </tool> |