Mercurial > repos > iuc > multiqc

comparison generate_test_data.sh @ 8:e0f4a651c6b9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
author iuc
date Fri, 20 Apr 2018 01:06:25 -0400
parents 3bad335ccea9
children df99138d2776
comparison
equal deleted inserted replaced
7:467486f1c568 8:e0f4a651c6b9
1 #!/usr/bin/env bash 1 #!/usr/bin/env bash
2 2
3 # 1st test 3 # 1st test
4 mkdir multiqc_WDir 4 mkdir -p 'multiqc_WDir/cutadapt'
5 5 cp 'test-data/cutadapt.txt' 'multiqc_WDir/cutadapt/cutadapt.txt'
6 mkdir 'multiqc_WDir/cutadapt_0' 6 sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt/cutadapt.txt'
7 cp 'test-data/cutadapt.txt' 'multiqc_WDir/cutadapt_0/cutadapt.txt' 7
8 sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/cutadapt.txt' 8 mkdir -p 'multiqc_WDir/fastqc/data_0/file_0'
9 9 cp 'test-data/fastqc_1.txt' 'multiqc_WDir/fastqc/data_0/file_0/fastqc_data.txt'
10 mkdir -p 'multiqc_WDir/fastqc_1/data_0/file_0' 10 mkdir -p 'multiqc_WDir/fastqc/data_0/file_1'
11 cp 'test-data/fastqc_1.txt' 'multiqc_WDir/fastqc_1/data_0/file_0/fastqc_data.txt' 11 cp 'test-data/fastqc_2.txt' 'multiqc_WDir/fastqc/data_0/file_1/fastqc_data.txt'
12 mkdir 'multiqc_WDir/fastqc_1/data_0/file_1' 12
13 cp 'test-data/fastqc_2.txt' 'multiqc_WDir/fastqc_1/data_0/file_1/fastqc_data.txt' 13 mkdir -p 'multiqc_WDir/flexbar'
14 14 cp 'test-data/flexbar.txt' 'multiqc_WDir/flexbar/flexbar.txt'
15 mkdir 'multiqc_WDir/flexbar_2' 15
16 cp 'test-data/flexbar.txt' 'multiqc_WDir/flexbar_2/flexbar.txt' 16 mkdir -p 'multiqc_WDir/sortmerna'
17 17 cp 'test-data/sortmerna.txt' 'multiqc_WDir/sortmerna/sortmerna.txt'
18 mkdir 'multiqc_WDir/sortmerna_3' 18
19 cp 'test-data/sortmerna.txt' 'multiqc_WDir/sortmerna_3/sortmerna.txt' 19 mkdir -p 'multiqc_WDir/trimmomatic'
20 20 cp 'test-data/trimmomatic.txt' 'multiqc_WDir/trimmomatic/trimmomatic.txt'
21 mkdir 'multiqc_WDir/trimmomatic_4'
22 cp 'test-data/trimmomatic.txt' 'multiqc_WDir/trimmomatic_4/trimmomatic.txt'
23 21
24 multiqc multiqc_WDir 22 multiqc multiqc_WDir
25 23
26 mv 'multiqc_report.html' 'test-data/pre_alignment_soft_report.html' 24 mv 'multiqc_report.html' 'test-data/pre_alignment_soft_report.html'
27 mv 'multiqc_data/multiqc.log' 'test-data/pre_alignment_soft_log.txt' 25 mv 'multiqc_data/multiqc.log' 'test-data/pre_alignment_soft_log.txt'
34 32
35 rm -rf 'multiqc_WDir' 33 rm -rf 'multiqc_WDir'
36 rm -rf 'multiqc_data/' 34 rm -rf 'multiqc_data/'
37 35
38 # 2nd test 36 # 2nd test
39 mkdir multiqc_WDir 37 mkdir -p 'multiqc_WDir/bismark'
40 38 cp 'test-data/bismark.txt' 'multiqc_WDir/bismark/bismark_SE_report.txt'
41 mkdir 'multiqc_WDir/bismark_0' 39
42 cp 'test-data/bismark.txt' 'multiqc_WDir/bismark_0/bismark_SE_report.txt' 40 mkdir -p 'multiqc_WDir/bowtie2'
43 41 cp 'test-data/bowtie2_1.txt' 'multiqc_WDir/bowtie2/bowtie2_1.txt'
44 mkdir 'multiqc_WDir/bowtie2_1' 42 cp 'test-data/bowtie2_2.txt' 'multiqc_WDir/bowtie2/bowtie2_2.txt'
45 cp 'test-data/bowtie2_1.txt' 'multiqc_WDir/bowtie2_1/bowtie2_1.txt' 43
46 cp 'test-data/bowtie2_2.txt' 'multiqc_WDir/bowtie2_1/bowtie2_2.txt' 44 mkdir -p 'multiqc_WDir/hisat2'
47 45 cp 'test-data/hisat2_1.txt' 'multiqc_WDir/hisat2/hisat2_1.txt'
48 mkdir 'multiqc_WDir/hisat2_3' 46 cp 'test-data/hisat2_2.txt' 'multiqc_WDir/hisat2/hisat2_2.txt'
49 cp 'test-data/hisat2_1.txt' 'multiqc_WDir/hisat2_3/hisat2_1.txt' 47
50 cp 'test-data/hisat2_2.txt' 'multiqc_WDir/hisat2_3/hisat2_2.txt' 48 mkdir -p 'multiqc_WDir/hicexplorer'
51 49 cp 'test-data/hicexplorer1.log' 'multiqc_WDir/hicexplorer/'
52 mkdir 'multiqc_WDir/kallisto_4' 50 cp 'test-data/hicexplorer2.log' 'multiqc_WDir/hicexplorer/'
53 cp 'test-data/kallisto_1.txt' 'multiqc_WDir/kallisto_4/kallisto_1.txt' 51
54 cp 'test-data/kallisto_2.txt' 'multiqc_WDir/kallisto_4/kallisto_2.txt' 52 mkdir -p 'multiqc_WDir/kallisto'
55 53 cp 'test-data/kallisto_1.txt' 'multiqc_WDir/kallisto/kallisto_1.txt'
56 mkdir -p 'multiqc_WDir/salmon_5/fld_0/file_0' 54 cp 'test-data/kallisto_2.txt' 'multiqc_WDir/kallisto/kallisto_2.txt'
57 cp 'test-data/salmon.txt' 'multiqc_WDir/salmon_5/fld_0/file_0/flenDist.txt' 55
58 56 #mkdir -p 'multiqc_WDir/salmon/fld_0/file_0'
59 mkdir -p 'multiqc_WDir/star_6/log_0' 57 #cp 'test-data/salmon_flenDist.txt' 'multiqc_WDir/salmon/fld_0/file_0/flenDist.txt'
60 cp 'test-data/star_log.txt' 'multiqc_WDir/star_6/log_0/star_log_Log.final.out' 58 #mkdir -p 'multiqc_WDir/salmon/fld_1/file_0'
61 mkdir 'multiqc_WDir/star_6/genecounts_1' 59 #cp 'test-data/salmon_meta_info.json' 'multiqc_WDir/salmon/fld_1/file_0/meta_info.json'
62 cp 'test-data/star_counts.txt' 'multiqc_WDir/star_6/genecounts_1/star_counts_ReadsPerGene.out.tab' 60
63 61 mkdir -p 'multiqc_WDir/star/log_0'
64 mkdir 'multiqc_WDir/tophat_7' 62 cp 'test-data/star_log.txt' 'multiqc_WDir/star/log_0/star_log_Log.final.out'
65 cp 'test-data/tophat.txt' 'multiqc_WDir/tophat_7/tophat_align_summary.txt' 63 mkdir -p 'multiqc_WDir/star/genecounts_1'
64 cp 'test-data/star_counts.txt' 'multiqc_WDir/star/genecounts_1/star_counts_ReadsPerGene.out.tab'
65
66 mkdir -p 'multiqc_WDir/tophat'
67 cp 'test-data/tophat.txt' 'multiqc_WDir/tophat/tophat_align_summary.txt'
66 68
67 multiqc multiqc_WDir 69 multiqc multiqc_WDir
68 70
69 mv 'multiqc_report.html' 'test-data/aligner_soft_report.html' 71 mv 'multiqc_report.html' 'test-data/aligner_soft_report.html'
70 mv 'multiqc_data/multiqc_bismark_alignment.txt' 'test-data/bismark_stats.tabular' 72 mv 'multiqc_data/multiqc_bismark_alignment.txt' 'test-data/bismark_stats.tabular'
77 79
78 rm -rf 'multiqc_WDir' 80 rm -rf 'multiqc_WDir'
79 rm -rf 'multiqc_data/' 81 rm -rf 'multiqc_data/'
80 82
81 # 3rd test 83 # 3rd test
82 mkdir multiqc_WDir 84 mkdir -p 'multiqc_WDir/bamtools'
83 85 cp 'test-data/bamtools.txt' 'multiqc_WDir/bamtools/bamtools.txt'
84 mkdir 'multiqc_WDir/bamtools_0' 86
85 cp 'test-data/bamtools.txt' 'multiqc_WDir/bamtools_0/bamtools.txt' 87 mkdir -p 'multiqc_WDir/bcftools'
86 88 cp 'test-data/bcftools.txt' 'multiqc_WDir/bcftools/bcftools.txt'
87 mkdir 'multiqc_WDir/bcftools_1' 89
88 cp 'test-data/bcftools.txt' 'multiqc_WDir/bcftools_1/bcftools.txt' 90 mkdir -p 'multiqc_WDir/busco'
89 91 cp 'test-data/busco.txt' 'multiqc_WDir/busco/short_summary_busco.txt'
90 mkdir 'multiqc_WDir/busco_2' 92
91 cp 'test-data/busco.txt' 'multiqc_WDir/busco_2/short_summary_busco.txt' 93 mkdir -p 'multiqc_WDir/deeptools'
92 94 cp 'test-data/deeptools_bamPEFragmentSize.txt' 'multiqc_WDir/deeptools/'
93 mkdir 'multiqc_WDir/featureCounts_3' 95 cp 'test-data/deeptools_estimateReadFiltering.txt' 'multiqc_WDir/deeptools/'
94 cp 'test-data/featureCounts.txt' 'multiqc_WDir/featureCounts_3/featureCounts.summary' 96 cp 'test-data/deeptools_plotCoverageOutRawCounts.txt' 'multiqc_WDir/deeptools/'
95 97 cp 'test-data/deeptools_plotCoverageStdout.txt' 'multiqc_WDir/deeptools/'
96 mkdir 'multiqc_WDir/gatk_4' 98 cp 'test-data/deeptools_plotEnrichment.txt' 'multiqc_WDir/deeptools/'
97 cp 'test-data/gatk_BaseRecalibrator.txt' 'multiqc_WDir/gatk_4/gatk_BaseRecalibrator.txt' 99 cp 'test-data/deeptools_plotFingerprintOutRawCounts.txt' 'multiqc_WDir/deeptools/'
98 cp 'test-data/gatk_varianteval.txt' 'multiqc_WDir/gatk_4/gatk_varianteval.txt' 100
99 101 mkdir -p 'multiqc_WDir/featureCounts'
100 mkdir 'multiqc_WDir/htseq_5' 102 cp 'test-data/featureCounts.txt' 'multiqc_WDir/featureCounts/featureCounts.summary'
101 cp 'test-data/htseq.txt' 'multiqc_WDir/htseq_5/htseq.txt' 103
102 104 mkdir -p 'multiqc_WDir/gatk'
103 mkdir 'multiqc_WDir/picard_6' 105 cp 'test-data/gatk_BaseRecalibrator.txt' 'multiqc_WDir/gatk/gatk_BaseRecalibrator.txt'
104 cp 'test-data/picard_collectGcBias.txt' 'multiqc_WDir/picard_6/picard_collectGcBias.txt' 106 cp 'test-data/gatk_varianteval.txt' 'multiqc_WDir/gatk/gatk_varianteval.txt'
105 cp 'test-data/picard_CollectInsertSizeMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectInsertSizeMetrics.txt' 107
106 cp 'test-data/picard_MarkDuplicates.txt' 'multiqc_WDir/picard_6/picard_MarkDuplicates.txt' 108 mkdir -p 'multiqc_WDir/htseq'
107 cp 'test-data/picard_CollectBaseDistributionByCycle.txt' 'multiqc_WDir/picard_6/picard_CollectBaseDistributionByCycle.txt' 109 cp 'test-data/htseq.txt' 'multiqc_WDir/htseq/htseq.txt'
108 cp 'test-data/picard_CollectRnaSeqMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectRnaSeqMetrics.txt' 110
109 cp 'test-data/picard_CollectAlignmentSummaryMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectAlignmentSummaryMetrics.txt' 111 mkdir -p 'multiqc_WDir/picard'
110 112 cp 'test-data/picard_collectGcBias.txt' 'multiqc_WDir/picard/picard_collectGcBias.txt'
111 mkdir 'multiqc_WDir/prokka_7' 113 cp 'test-data/picard_CollectInsertSizeMetrics.txt' 'multiqc_WDir/picard/picard_CollectInsertSizeMetrics.txt'
112 cp 'test-data/prokka_1.txt' 'multiqc_WDir/prokka_7/prokka_1.txt' 114 cp 'test-data/picard_MarkDuplicates.txt' 'multiqc_WDir/picard/picard_MarkDuplicates.txt'
113 cp 'test-data/prokka_2.txt' 'multiqc_WDir/prokka_7/prokka_2.txt' 115 cp 'test-data/picard_CollectBaseDistributionByCycle.txt' 'multiqc_WDir/picard/picard_CollectBaseDistributionByCycle.txt'
114 116 cp 'test-data/picard_CollectRnaSeqMetrics.txt' 'multiqc_WDir/picard/picard_CollectRnaSeqMetrics.txt'
115 mkdir -p 'multiqc_WDir/quast_8/file_0' 117 cp 'test-data/picard_CollectAlignmentSummaryMetrics.txt' 'multiqc_WDir/picard/picard_CollectAlignmentSummaryMetrics.txt'
116 cp 'test-data/quast.tsv' 'multiqc_WDir/quast_8/file_0/report.tsv' 118
117 119 mkdir -p 'multiqc_WDir/prokka'
118 #mkdir 'multiqc_WDir/rsem_9' 120 cp 'test-data/prokka_1.txt' 'multiqc_WDir/prokka/prokka_1.txt'
119 #cp 'test-data/rsem.txt' 'multiqc_WDir/rsem_9/rsem.cnt' 121 cp 'test-data/prokka_2.txt' 'multiqc_WDir/prokka/prokka_2.txt'
120 122
121 mkdir -p 'multiqc_WDir/rseqc_10/read_gc_0' 123 mkdir -p 'multiqc_WDir/quast/file_0'
122 cp 'test-data/rseqc.txt' 'multiqc_WDir/rseqc_10/read_gc_0/rseq.GC.xls' 124 cp 'test-data/quast.tsv' 'multiqc_WDir/quast/file_0/report.tsv'
123 125
124 mkdir 'multiqc_WDir/samblaster_11' 126 #mkdir -p 'multiqc_WDir/rsem'
125 cp 'test-data/samblaster.txt' 'multiqc_WDir/samblaster_11/samblaster.txt' 127 #cp 'test-data/rsem.txt' 'multiqc_WDir/rsem/rsem.cnt'
126 128
127 mkdir -p 'multiqc_WDir/samtools_12/stats_0' 129 mkdir -p 'multiqc_WDir/rseqc/read_gc_0'
128 cp 'test-data/samtools_stats.txt' 'multiqc_WDir/samtools_12/stats_0/samtools_stats.txt' 130 cp 'test-data/rseqc.txt' 'multiqc_WDir/rseqc/read_gc_0/rseq.GC.xls'
129 mkdir 'multiqc_WDir/samtools_12/flagstat_1' 131
130 cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools_12/flagstat_1/samtools_flagstat.txt' 132 mkdir -p 'multiqc_WDir/samblaster'
131 mkdir 'multiqc_WDir/samtools_12/idxstats_2' 133 cp 'test-data/samblaster.txt' 'multiqc_WDir/samblaster/samblaster.txt'
132 cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools_12/idxstats_2/samtools_idxstats_idxstat' 134
133 135 mkdir -p 'multiqc_WDir/samtools/stats_0'
134 #mkdir 'multiqc_WDir/snpeff_13' 136 cp 'test-data/samtools_stats.txt' 'multiqc_WDir/samtools/stats_0/samtools_stats.txt'
135 #cp 'test-data/snpeff.csv' 'multiqc_WDir/snpeff_13/snpeff.txt' 137 mkdir -p 'multiqc_WDir/samtools/flagstat_1'
136 138 cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools/flagstat_1/samtools_flagstat.txt'
137 mkdir -p 'multiqc_WDir/vcftools_14/tstv_by_qual_0' 139 mkdir -p 'multiqc_WDir/samtools/idxstats_2'
138 cp 'test-data/vcftools.txt' 'multiqc_WDir/vcftools_14/tstv_by_qual_0/vcftools.TsTv.qual' 140 cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools/idxstats_2/samtools_idxstats_idxstat'
141
142 mkdir -p 'multiqc_WDir/snpeff'
143 cp 'test-data/snpeff.csv' 'multiqc_WDir/snpeff/snpeff.txt'
144
145 mkdir -p 'multiqc_WDir/vcftools/tstv_by_qual_0'
146 cp 'test-data/vcftools.txt' 'multiqc_WDir/vcftools/tstv_by_qual_0/vcftools.TsTv.qual'
139 147
140 multiqc multiqc_WDir 148 multiqc multiqc_WDir
141 149
142 mv 'multiqc_report.html' 'test-data/post_aligner_soft_report.html' 150 mv 'multiqc_report.html' 'test-data/post_aligner_soft_report.html'
143 mv 'multiqc_data/multiqc_bamtools_stats.txt' 'test-data/bamtools_stats.tabular' 151 mv 'multiqc_data/multiqc_bamtools_stats.txt' 'test-data/bamtools_stats.tabular'
153 mv 'multiqc_data/multiqc_picard_dups.txt' 'test-data/picard_dups_stats.tabular' 161 mv 'multiqc_data/multiqc_picard_dups.txt' 'test-data/picard_dups_stats.tabular'
154 mv 'multiqc_data/multiqc_picard_insertSize.txt' 'test-data/picard_insertSize_stats.tabular' 162 mv 'multiqc_data/multiqc_picard_insertSize.txt' 'test-data/picard_insertSize_stats.tabular'
155 mv 'multiqc_data/multiqc_prokka.txt' 'test-data/prokka_stats.tabular' 163 mv 'multiqc_data/multiqc_prokka.txt' 'test-data/prokka_stats.tabular'
156 mv 'multiqc_data/multiqc_quast.txt' 'test-data/quast_stats.tabular' 164 mv 'multiqc_data/multiqc_quast.txt' 'test-data/quast_stats.tabular'
157 #mv 'multiqc_data/multiqc_rsem.txt' 'test-data/rsem_stats.tabular' 165 #mv 'multiqc_data/multiqc_rsem.txt' 'test-data/rsem_stats.tabular'
158 mv 'multiqc_data/multiqc_rseqc.txt' 'test-data/rseqc_stats.tabular'
159 mv 'multiqc_data/multiqc_samblaster.txt' 'test-data/samblaster_stats.tabular' 166 mv 'multiqc_data/multiqc_samblaster.txt' 'test-data/samblaster_stats.tabular'
160 mv 'multiqc_data/multiqc_samtools_flagstat.txt' 'test-data/samtools_flagstat_stats.tabular' 167 mv 'multiqc_data/multiqc_samtools_flagstat.txt' 'test-data/samtools_flagstat_stats.tabular'
161 mv 'multiqc_data/multiqc_samtools_stats.txt' 'test-data/samtools_stats_stats.tabular' 168 mv 'multiqc_data/multiqc_samtools_stats.txt' 'test-data/samtools_stats_stats.tabular'
162 #mv 'multiqc_data/multiqc_snpeff.txt' 'test-data/snpeff_stats.tabular' 169 mv 'multiqc_data/multiqc_snpeff.txt' 'test-data/snpeff_stats.tabular'
163 170
164 rm -rf 'multiqc_WDir' 171 rm -rf 'multiqc_WDir'
165 rm -rf 'multiqc_data/' 172 rm -rf 'multiqc_data/'
166 173
167 # 4th test 174 # 4th test
168 mkdir multiqc_WDir 175 mkdir -p 'multiqc_WDir/custom_content_0'
169
170 mkdir 'multiqc_WDir/custom_content_0'
171 cp 'test-data/cc_ko15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_0.tsv' 176 cp 'test-data/cc_ko15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_0.tsv'
172 cp 'test-data/cc_wt15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_1.tsv' 177 cp 'test-data/cc_wt15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_1.tsv'
173 178
174 echo "custom_data:" > 'config_file' 179 echo "custom_data:" > 'config_file'
175 echo " section_0:" >> 'config_file' 180 echo " section_0:" >> 'config_file'