|
0
|
1 <tool id='differential_expression' name='Differential Expression' version='1.0'>
|
|
|
2 <description>Generates results for DE </description>
|
|
|
3 <!--requirement></requirement-->
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
|
|
|
6 <requirement type="set_environment">TRINITY_HOME</requirement>
|
|
|
7
|
|
|
8 </requirements>
|
|
|
9 <command>
|
|
|
10
|
|
|
11 echo -e "Differential Expression Log File" > $output_log 2>&1;
|
|
|
12
|
|
|
13 ## Step 0: preprocess input_file preparaton
|
|
|
14
|
|
|
15 #for $i in $isoform_sample:
|
|
|
16 cp -s $i.isoform_sample_matrix $i.sample_name;
|
|
|
17 #end for;
|
|
|
18
|
|
|
19
|
|
|
20 ## Step 1: abundance_estimates_to_matrix
|
|
|
21 echo -e "" >> $output_log 2>&1;
|
|
|
22 echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" >> $output_log 2>&1;
|
|
|
23 echo -e "\#\# Step 1: abundance_estimates_to_matrix" >> $output_log 2>&1;
|
|
|
24 echo -e "" >> $output_log 2>&1;
|
|
|
25
|
|
|
26
|
|
|
27 perl \$TRINITY_HOME/util/abundance_estimates_to_matrix.pl
|
|
|
28 --est_method $est_method
|
|
|
29 #for $i in $isoform_sample:
|
|
|
30 $i.sample_name
|
|
|
31 #end for
|
|
|
32 >> $output_log 2>&1;
|
|
|
33
|
|
|
34
|
|
|
35 ## Step 2: run_DE_analysis
|
|
|
36 echo -e "" >> $output_log 2>&1;
|
|
|
37 echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" >> $output_log 2>&1;
|
|
|
38 echo -e "\#\# Step 2: run_DE_analysis" >> $output_log 2>&1;
|
|
|
39 echo -e "" >> $output_log 2>&1;
|
|
|
40
|
|
|
41 perl \$TRINITY_HOME/Analysis/DifferentialExpression/run_DE_analysis.pl
|
|
|
42 --matrix matrix.counts.matrix
|
|
|
43 --method $method
|
|
|
44 --output result_dir
|
|
|
45 >> $output_log 2>&1;
|
|
|
46
|
|
|
47 ## Step 3: analyze_diff_expr
|
|
|
48 echo -e "" >> $output_log 2>&1;
|
|
|
49 echo -e "\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#" >> $output_log 2>&1;
|
|
|
50 echo -e "\#\# Step 3: analyze_diff_expr" >> $output_log 2>&1;
|
|
|
51 echo -e "" >> $output_log 2>&1;
|
|
|
52
|
|
|
53 cd result_dir && perl \$TRINITY_HOME/Analysis/DifferentialExpression/analyze_diff_expr.pl
|
|
|
54
|
|
|
55 --matrix ../matrix.TMM.fpkm.matrix
|
|
|
56
|
|
|
57 >> $output_log 2>&1;
|
|
|
58
|
|
|
59 pwd;
|
|
|
60 cd .. && zip -r results.zip result_dir;
|
|
|
61 </command>
|
|
|
62
|
|
|
63 <inputs>
|
|
|
64 <!-- Required -->
|
|
|
65
|
|
|
66 <param name='est_method' type='select' display="radio" label='Select est_method'>
|
|
|
67 <option value="RSEM" selected='true'>RSEM</option>
|
|
|
68 <option value="eXpress">eXpress</option>
|
|
|
69 </param>
|
|
|
70
|
|
|
71
|
|
|
72 <repeat name="isoform_sample" title="Isoform Sample" min="2">
|
|
|
73 <param name="sample_name" type="text" label="Sample Name" help="Only alpha-numerical name without space.">
|
|
|
74 <validator type="empty_field" message="don't leave the field empty!"/>
|
|
|
75 </param>
|
|
|
76 <param format="tabular" name="isoform_sample_matrix" type="data" label="Isoform Sample Matrix"/>
|
|
|
77 </repeat>
|
|
|
78
|
|
|
79 <param name='method' type="select" label="Select Method" >
|
|
|
80 <option value="edgeR">edgeR</option>
|
|
|
81 <option value="DESeq">DESeq</option>
|
|
|
82 <option value="DESeq2">DESeq2</option>
|
|
|
83 </param>
|
|
|
84
|
|
|
85
|
|
|
86
|
|
|
87 <!-- Optional -->
|
|
|
88
|
|
|
89 </inputs>
|
|
|
90 <outputs>
|
|
|
91 <data name='de_output' format='zip' label="${tool.name} on ${on_string}: compressed_output" from_work_dir="results.zip"/>
|
|
|
92 <data name='output_log' format='txt' label="${tool.name} on ${on_string} : matrix_log"/>
|
|
|
93 </outputs>
|
|
|
94 </tool>
|
