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comparison samples_qccheck.xml @ 2:1317615eff73 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3c4a2b13b0f3a280de4f98f4f5e0dc29e10fc7a0
author iuc
date Tue, 29 Mar 2016 06:46:09 -0400
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1:fd94a21c2131 2:1317615eff73
1 <tool id="samples_qccheck" name="RNASeq samples quality check" version="2.1.1">
2 <description>for transcript quantification</description>
3 <requirements>
4 <requirement type="package" version="2.1.1">trinity</requirement>
5 <requirement type="package" version="2.30.0">bioconductor-biobase</requirement>
6 <requirement type="package" version="2.2.2">bioconductor-qvalue</requirement>
7 </requirements>
8 <stdio>
9 <exit_code range="1:"/>
10 </stdio>
11 <command><![CDATA[
12
13 ln -s "${matrix}" "input.matrix"
14
15 &&
16
17 PtR
18 --matrix "input.matrix"
19
20 --samples "${samples}"
21
22 --CPM --log2 --compare_replicates
23
24 &&
25
26 PtR
27 --matrix "input.matrix"
28
29 --samples "${samples}"
30
31 --CPM --log2 --sample_cor_matrix
32
33 &&
34
35 PtR
36 --matrix "input.matrix"
37
38 --samples "${samples}"
39
40 --CPM --log2 --prin_comp 3
41
42 && mkdir out_pdf
43 && mv *rep_compare.pdf out_pdf/
44 && mv *sample_cor_matrix.pdf out_pdf/
45 && mv *principal_components.pdf out_pdf/
46
47 ]]></command>
48 <inputs>
49 <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
50 <param format="tabular" name="samples" type="data" label="Samples description" help="file describing samples and replicates"/>
51 </inputs>
52 <outputs>
53 <collection name="reports" type="list" label="Quality check result files on ${on_string}">
54 <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" visible="true" />
55 </collection>
56 </outputs>
57 <tests>
58 <test>
59 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
60 <param name="samples" value="count/samples.txt"/>
61 <output_collection name="reports">
62 <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/>
63 <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/>
64 <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/>
65 <element name="input.matrix.minCol10.minRow10.CPM.log2.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.principal_components.pdf"/>
66 <element name="input.matrix.minCol10.minRow10.CPM.log2.sample_cor_matrix.pdf" compare="sim_size" delta="100" file="count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.sample_cor_matrix.pdf"/>
67 </output_collection>
68 </test>
69 </tests>
70 <help>
71 <![CDATA[
72 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
73 This tool performs some Quality Checks on a RNASeq experiment, analysing the abundance estimation for different samples using a transcriptome assembled with Trinity.
74
75 **Inputs**
76
77 This tool uses the matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
78
79 You must describe your samples and replicates with a tabular file looking like this:
80
81 =========== ================
82 ConditionA CondA_replicate1
83 ----------- ----------------
84 ConditionA CondA_replicate2
85 ----------- ----------------
86 ConditionB CondB_replicate1
87 ----------- ----------------
88 ConditionB CondB_replicate2
89 ----------- ----------------
90 ConditionC CondC_replicate1
91 ----------- ----------------
92 ConditionC CondC_replicate2
93 ----------- ----------------
94 ConditionC CondC_replicate3
95 =========== ================
96
97 The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'.
98
99 **Output**
100
101 This tool will produce several PDF files, see the following page for more information:
102
103 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/QC-Samples-and-Replicates
104
105
106 .. _Trinity: http://trinityrnaseq.github.io
107 ]]>
108 </help>
109
110 <citations>
111 <citation type="doi">doi:10.1038/nbt.1883</citation>
112 </citations>
113 </tool>
114