Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix
annotate abundance_estimates_to_matrix.xml @ 1:fba77b1f69b4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
author | iuc |
---|---|
date | Fri, 18 Nov 2016 06:07:28 -0500 |
parents | 77fc547df6ff |
children | 8b5039bdf1f6 |
rev | line source |
---|---|
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents:
0
diff
changeset
|
1 <tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.1"> |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
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
parents:
diff
changeset
|
3 <macros> |
77fc547df6ff
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> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
5 </macros> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
6 <expand macro="requirements"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
7 <requirement type="package" version="3.14.0">bioconductor-edger</requirement> |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents:
0
diff
changeset
|
8 <requirement type="package" version="0.7.2">salmon</requirement> |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
9 </expand> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
10 <expand macro="stdio"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
11 <command><![CDATA[ |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents:
0
diff
changeset
|
12 #import re |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
13 #for $entry in $samples: |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents:
0
diff
changeset
|
14 ln -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
15 #end for |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
16 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
17 abundance_estimates_to_matrix.pl |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
18 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
19 --est_method ${est_method} |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
20 --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
parents:
diff
changeset
|
21 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
22 #for $entry in $samples: |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents:
0
diff
changeset
|
23 '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
24 #end for |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
25 ]]></command> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
26 <inputs> |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents:
0
diff
changeset
|
27 <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" /> |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
28 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
29 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
30 <option value="RSEM">RSEM</option> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
31 <option value="eXpress">eXpress</option> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
32 <option value="salmon">Salmon</option> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
33 </param> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
34 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
35 <section name="additional_params" title="Additional Options" expanded="False"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
36 <param type="select" name="cross_sample_norm" argument="--cross_sample_norm" label="Cross sample normalization"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
37 <option value="TMM">TMM</option> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
38 <option value="UpperQuartile">UpperQuartile</option> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
39 <option value="none">None</option> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
40 </param> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
41 </section> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
42 </inputs> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
43 <outputs> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
44 <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment counts (raw counts)" from_work_dir="matrix.counts.matrix"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
45 <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of TPM expression values (not cross-sample normalized)" from_work_dir="matrix.TPM.not_cross_norm"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
46 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values" from_work_dir="matrix.TMM.EXPR.matrix"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
47 <filter>additional_params['cross_sample_norm'] == "TMM"</filter> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
48 </data> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
49 <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values" from_work_dir="matrix.UpperQuartile.EXPR.matrix"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
50 <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
parents:
diff
changeset
|
51 </data> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
52 </outputs> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
53 <tests> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
54 <test> |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents:
0
diff
changeset
|
55 <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
parents:
diff
changeset
|
56 <param name="est_method" value="RSEM"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
57 <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
parents:
diff
changeset
|
58 <output name="trans_counts"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
59 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
60 <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
parents:
diff
changeset
|
61 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
62 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
63 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
64 <output name="TPM_no_norm"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
65 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
66 <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
parents:
diff
changeset
|
67 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
68 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
69 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
70 <output name="norm"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
71 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
72 <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
parents:
diff
changeset
|
73 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
74 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
75 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
76 </test> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
77 <test> |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents:
0
diff
changeset
|
78 <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
parents:
diff
changeset
|
79 <param name="est_method" value="RSEM"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
80 <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
parents:
diff
changeset
|
81 <output name="trans_counts"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
82 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
83 <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
parents:
diff
changeset
|
84 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
85 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
86 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
87 <output name="TPM_no_norm"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
88 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
89 <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
parents:
diff
changeset
|
90 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
91 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
92 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
93 <output name="norm"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
94 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
95 <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
parents:
diff
changeset
|
96 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
97 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
98 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
99 </test> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
100 <test> |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents:
0
diff
changeset
|
101 <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
iuc
parents:
diff
changeset
|
102 <param name="est_method" value="eXpress"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
103 <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
parents:
diff
changeset
|
104 <output name="trans_counts"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
105 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
106 <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
parents:
diff
changeset
|
107 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
108 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
109 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
110 <output name="TPM_no_norm"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
111 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
112 <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
parents:
diff
changeset
|
113 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
114 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
115 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
116 <output name="norm"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
117 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
118 <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
parents:
diff
changeset
|
119 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
120 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
121 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
122 </test> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
123 <test> |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents:
0
diff
changeset
|
124 <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
parents:
diff
changeset
|
125 <param name="est_method" value="RSEM"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
126 <param name="cross_sample_norm" value="UpperQuartile"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
127 <output name="trans_counts"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
128 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
129 <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
parents:
diff
changeset
|
130 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
131 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
132 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
133 <output name="TPM_no_norm"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
134 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
135 <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
parents:
diff
changeset
|
136 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
137 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
138 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
139 <output name="norm"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
140 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
141 <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
parents:
diff
changeset
|
142 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
143 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
144 </test> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
145 <test> |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents:
0
diff
changeset
|
146 <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
parents:
diff
changeset
|
147 <param name="est_method" value="RSEM"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
148 <param name="cross_sample_norm" value="none"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
149 <output name="trans_counts"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
150 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
151 <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
parents:
diff
changeset
|
152 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
153 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
154 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
155 <output name="TPM_no_norm"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
156 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
157 <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
parents:
diff
changeset
|
158 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
159 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
160 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
161 </test> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
162 <test> |
1
fba77b1f69b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
iuc
parents:
0
diff
changeset
|
163 <param name="samples" ftype="tabular" value="count/salmon/sample_A,count/salmon/sample_B"/> |
0
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
164 <param name="est_method" value="salmon"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
165 <param name="cross_sample_norm" value="none"/> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
166 <output name="trans_counts"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
167 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
168 <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
parents:
diff
changeset
|
169 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
170 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
171 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
172 <output name="TPM_no_norm"> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
173 <assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
174 <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
parents:
diff
changeset
|
175 <has_n_columns n="3" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
176 </assert_contents> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
177 </output> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
178 </test> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
179 </tests> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
180 <help> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
181 <![CDATA[ |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
182 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
183 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. |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
184 This matrix can then be used by 'RNASeq samples quality check for transcript quantification' and 'Differential Expression Analysis using a Trinity assembly' tools. |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
185 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
186 **Inputs** |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
187 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
188 It takes as input multiple results from 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool/ |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
189 Each sample must have a name, that should be used in subsequent tools. |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
190 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
191 **Output** |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
192 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
193 This tool will produce a single matrix file. More details on this page: |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
194 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
195 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
196 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
197 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
198 .. _Trinity: http://trinityrnaseq.github.io |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
199 ]]> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
200 </help> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
201 |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
202 <expand macro="citation" /> |
77fc547df6ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff
changeset
|
203 </tool> |