Mercurial > repos > pjbriggs > rnachipintegrator

comparison make_test_data.sh @ 0:0abe6bac47a6 draft

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planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
author pjbriggs
date Wed, 24 Feb 2016 09:25:18 -0500
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-1:000000000000 0:0abe6bac47a6
1 #!/bin/bash -e
2 #
3 # List of dependencies
4 TOOL_DEPENDENCIES="rnachipintegrator/0.5.0-alpha.7
5 xlsxwriter/0.8.4"
6 # Where to find them
7 TOOL_DEPENDENCIES_DIR=$(pwd)/test.tool_dependencies.rnachipintegrator
8 if [ ! -d $TOOL_DEPENDENCIES_DIR ] ; then
9 echo WARNING $TOOL_DEPENDENCIES_DIR not found >&2
10 echo Creating tool dependencies dir
11 mkdir -p $TOOL_DEPENDENCIES_DIR
12 echo Installing tool dependencies
13 $(dirname $0)/install_tool_deps.sh $TOOL_DEPENDENCIES_DIR
14 fi
15 # Load dependencies
16 for dep in $TOOL_DEPENDENCIES ; do
17 env_file=$TOOL_DEPENDENCIES_DIR/$dep/env.sh
18 if [ -e $env_file ] ; then
19 . $env_file
20 else
21 echo ERROR no env.sh file found for $dep >&2
22 exit 1
23 fi
24 done
25 #
26 # rnachipintegrator_canonical_genes
27 #
28 # Test #1
29 RnaChipIntegrator --name=mm9 \
30 --cutoff=50000 \
31 --number=4 \
32 --xlsx \
33 --compact \
34 test-data/mm9_canonical_genes.tsv test-data/mm9_summits.txt
35 mv mm9_gene_centric.txt test-data/mm9_summits_per_feature.out
36 mv mm9_peak_centric.txt test-data/mm9_features_per_summit.out
37 mv mm9.xlsx test-data/mm9_summits.xlsx
38 #
39 # Test #2
40 RnaChipIntegrator --name=mm9 \
41 --cutoff=50000 \
42 --number=4 \
43 --xlsx \
44 --compact \
45 test-data/mm9_canonical_genes.tsv test-data/mm9_peaks.txt
46 mv mm9_gene_centric.txt test-data/mm9_peaks_per_feature1.out
47 mv mm9_peak_centric.txt test-data/mm9_features_per_peak1.out
48 mv mm9.xlsx test-data/mm9_peaks1.xlsx
49 #
50 # Test #3
51 RnaChipIntegrator --name=mm9 \
52 --cutoff=50000 \
53 --number=4 \
54 --xlsx \
55 --summary \
56 --pad \
57 test-data/mm9_canonical_genes.tsv test-data/mm9_peaks.txt
58 mv mm9_gene_centric.txt test-data/mm9_peaks_per_feature3.out
59 mv mm9_peak_centric.txt test-data/mm9_features_per_peak3.out
60 mv mm9_gene_centric_summary.txt test-data/mm9_peaks_per_feature3.summary
61 mv mm9_peak_centric_summary.txt test-data/mm9_features_per_peak3.summary
62 mv mm9.xlsx test-data/mm9_peaks3.xlsx
63 #
64 # rnachipintegrator_wrapper
65 #
66 # Test #1
67 RnaChipIntegrator --name=test \
68 --cutoff=130000 \
69 --number=4 \
70 --promoter_region=-10000,2500 \
71 --xlsx \
72 --compact \
73 test-data/features.txt test-data/summits.txt
74 mv test_gene_centric.txt test-data/summits_per_feature.out
75 mv test_peak_centric.txt test-data/features_per_summit.out
76 mv test.xlsx test-data/summits.xlsx
77 #
78 # Test #2
79 RnaChipIntegrator --name=test \
80 --cutoff=130000 \
81 --number=4 \
82 --promoter_region=-10000,2500 \
83 --xlsx \
84 --compact \
85 test-data/features.txt test-data/peaks.txt
86 mv test_gene_centric.txt test-data/peaks_per_feature1.out
87 mv test_peak_centric.txt test-data/features_per_peak1.out
88 mv test.xlsx test-data/peaks1.xlsx
89 #
90 # Test #3
91 RnaChipIntegrator --name=test \
92 --cutoff=130000 \
93 --number=4 \
94 --xlsx \
95 test-data/features.txt test-data/peaks.txt
96 mv test_gene_centric.txt test-data/peaks_per_feature2.out
97 mv test_peak_centric.txt test-data/features_per_peak2.out
98 mv test.xlsx test-data/peaks2.xlsx
99 #
100 # Test #4
101 RnaChipIntegrator --name=test \
102 --cutoff=130000 \
103 --number=4 \
104 --only-DE \
105 --xlsx \
106 --compact \
107 test-data/features.txt test-data/peaks.txt
108 mv test_gene_centric.txt test-data/peaks_per_feature3.out
109 mv test_peak_centric.txt test-data/features_per_peak3.out
110 mv test.xlsx test-data/peaks3.xlsx
111 #
112 # Test #5
113 RnaChipIntegrator --name=test \
114 --cutoff=130000 \
115 --number=4 \
116 --xlsx \
117 --summary \
118 --pad \
119 test-data/features.txt test-data/peaks.txt
120 mv test_gene_centric.txt test-data/peaks_per_feature4.out
121 mv test_peak_centric.txt test-data/features_per_peak4.out
122 mv test_gene_centric_summary.txt test-data/peaks_per_feature4.summary
123 mv test_peak_centric_summary.txt test-data/features_per_peak4.summary
124 mv test.xlsx test-data/peaks4.xlsx
125 ##
126 #