Mercurial > repos > pjbriggs > rnachipintegrator

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