Mercurial > repos > iuc > trinity_filter_low_expr_transcripts
annotate filter_low_expr_transcripts.xml @ 6:4c01c7697420 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
author | iuc |
---|---|
date | Mon, 28 Aug 2017 16:55:37 -0400 |
parents | 30d6a6424102 |
children | e659504d166c |
rev | line source |
---|---|
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
1 <tool id="trinity_filter_low_expr_transcripts" name="Filter low expression transcripts" version="@WRAPPER_VERSION@.0"> |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
2 <description>from a Trinity assembly</description> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
3 <macros> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
4 <import>macros.xml</import> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
5 </macros> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
6 <expand macro="requirements"/> |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
7 <command detect_errors="aggressive"><![CDATA[ |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
8 filter_low_expr_transcripts.pl |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
9 --matrix '$matrix' |
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
10 --transcripts '$assembly' |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
11 |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
12 #if $additional_params.gene_map.has_gene_map == "no": |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
13 --gene_to_trans_map '$additional_params.gene_map.gene_trans_map' |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
14 #else |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
15 --trinity_mode |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
16 #end if |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
17 |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
18 #if str($min_expr_any): |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
19 --min_expr_any $min_expr_any |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
20 #end if |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
21 |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
22 #if str($isoform_filter.isoform_mode) == "highest_iso_only": |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
23 --highest_iso_only |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
24 #else if str($isoform_filter.isoform_mode) == "min_pct_dom_iso": |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
25 --min_pct_dom_iso $isoform_filter.min_pct_dom_iso |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
26 #end if |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
27 |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
28 > '$filtered' |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
29 ]]></command> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
30 <inputs> |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
31 <param argument="--transcripts" name="assembly" type="data" format="fasta" label="Trinity assembly"/> |
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
32 <param argument="--matrix" type="data" format="tabular" label="Expression matrix"/> |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
33 |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
34 <param name="min_expr_any" type="float" argument="--min_expr_any" optional="true" label="Minimum expression level required across any sample"/> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
35 |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
36 <conditional name="isoform_filter"> |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
37 <param name="isoform_mode" type="select" label="Isoform filtering method"> |
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
38 <option value="none">No filtering at the isoform level</option> |
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
39 <option value="highest_iso_only">Keep only the most highly expressed isoform per gene</option> |
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
40 <option value="min_pct_dom_iso">Keep all isoforms above a minimum percent of dominant expression</option> |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
41 </param> |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
42 <when value="none" /> |
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
43 <when value="highest_iso_only" /> |
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
44 <when value="min_pct_dom_iso"> |
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
45 <param argument="--min_pct_dom_iso" type="integer" value="" label="Minimum percent of dominant isoform expression"/> |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
46 </when> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
47 </conditional> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
48 |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
49 <section name="additional_params" title="Additional Options" expanded="False"> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
50 <conditional name="gene_map"> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
51 <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed"> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
52 <option value="yes">Yes</option> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
53 <option value="no">No</option> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
54 </param> |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
55 <when value="yes" /> |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
56 <when value="no"> |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
57 <param argument="--gene_to_trans_map" name="gene_trans_map" type="data" format="tabular" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" /> |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
58 </when> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
59 </conditional> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
60 |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
61 </section> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
62 </inputs> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
63 <outputs> |
4
e34706d4e786
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
iuc
parents:
1
diff
changeset
|
64 <data format="fasta" name="filtered" label="${tool.name} on ${on_string}: filtered low expression transcripts"/> |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
65 </outputs> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
66 <tests> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
67 <test> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
68 <param name="matrix" value="filtered/counts.matrix"/> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
69 <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
70 <param name="min_expr_any" value="25"/> |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
71 <param name="isoform_filter|isoform_mode" value="none"/> |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
72 <output name="filtered" file="filtered/Trinity_filtered_exp.fasta" /> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
73 </test> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
74 <test> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
75 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
76 <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/> |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
77 <param name="isoform_filter|isoform_mode" value="highest_iso_only"/> |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
78 <output name="filtered" file="filtered/Trinity_filtered_hi_iso.fasta" /> |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
79 </test> |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
80 <test> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
81 <param name="matrix" value="filtered/counts.matrix"/> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
82 <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/> |
5
30d6a6424102
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents:
4
diff
changeset
|
83 <param name="isoform_filter|isoform_mode" value="min_pct_dom_iso"/> |
0
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
84 <param name="isoform_filter|min_pct_dom_iso" value="20"/> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
85 <output name="filtered" file="filtered/Trinity_filtered_pct_iso.fasta" /> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
86 </test> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
87 </tests> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
88 <help> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
89 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
90 This tool filters a Trinity assembly using an expression matrix built |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
91 with "Build expression matrix for a de novo assembly of RNA-Seq data by Trinity" tool. |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
92 It discards transcripts/isoforms having a low expression level. |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
93 |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
94 .. _Trinity: http://trinityrnaseq.github.io |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
95 </help> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
96 |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
97 <expand macro="citation" /> |
6821f5ea01d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
98 </tool> |