Mercurial > repos > iuc > multiqc

comparison generate_test_data.sh @ 0:3bad335ccea9 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 264fd61d39f252ebb81731bf6cd3349fdb39b306
author iuc
date Tue, 24 Oct 2017 06:29:59 -0400
parents
children e0f4a651c6b9
comparison
equal deleted inserted replaced
-1:000000000000 0:3bad335ccea9
1 #!/usr/bin/env bash
2
3 # 1st test
4 mkdir multiqc_WDir
5
6 mkdir 'multiqc_WDir/cutadapt_0'
7 cp 'test-data/cutadapt.txt' 'multiqc_WDir/cutadapt_0/cutadapt.txt'
8 sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/cutadapt.txt'
9
10 mkdir -p 'multiqc_WDir/fastqc_1/data_0/file_0'
11 cp 'test-data/fastqc_1.txt' 'multiqc_WDir/fastqc_1/data_0/file_0/fastqc_data.txt'
12 mkdir 'multiqc_WDir/fastqc_1/data_0/file_1'
13 cp 'test-data/fastqc_2.txt' 'multiqc_WDir/fastqc_1/data_0/file_1/fastqc_data.txt'
14
15 mkdir 'multiqc_WDir/flexbar_2'
16 cp 'test-data/flexbar.txt' 'multiqc_WDir/flexbar_2/flexbar.txt'
17
18 mkdir 'multiqc_WDir/sortmerna_3'
19 cp 'test-data/sortmerna.txt' 'multiqc_WDir/sortmerna_3/sortmerna.txt'
20
21 mkdir 'multiqc_WDir/trimmomatic_4'
22 cp 'test-data/trimmomatic.txt' 'multiqc_WDir/trimmomatic_4/trimmomatic.txt'
23
24 multiqc multiqc_WDir
25
26 mv 'multiqc_report.html' 'test-data/pre_alignment_soft_report.html'
27 mv 'multiqc_data/multiqc.log' 'test-data/pre_alignment_soft_log.txt'
28 mv 'multiqc_data/multiqc_cutadapt.txt' 'test-data/cutadapt_stats.tabular'
29 mv 'multiqc_data/multiqc_fastqc.txt' 'test-data/fastqc_stats.tabular'
30 mv 'multiqc_data/multiqc_flexbar.txt' 'test-data/flexbar_stats.tabular'
31 mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/pre_alignment_soft_stats.tabular'
32 mv 'multiqc_data/multiqc_sortmerna.txt' 'test-data/sortmerna_stats.tabular'
33 mv 'multiqc_data/multiqc_trimmomatic.txt' 'test-data/trimmomatic_stats.tabular'
34
35 rm -rf 'multiqc_WDir'
36 rm -rf 'multiqc_data/'
37
38 # 2nd test
39 mkdir multiqc_WDir
40
41 mkdir 'multiqc_WDir/bismark_0'
42 cp 'test-data/bismark.txt' 'multiqc_WDir/bismark_0/bismark_SE_report.txt'
43
44 mkdir 'multiqc_WDir/bowtie2_1'
45 cp 'test-data/bowtie2_1.txt' 'multiqc_WDir/bowtie2_1/bowtie2_1.txt'
46 cp 'test-data/bowtie2_2.txt' 'multiqc_WDir/bowtie2_1/bowtie2_2.txt'
47
48 mkdir 'multiqc_WDir/hisat2_3'
49 cp 'test-data/hisat2_1.txt' 'multiqc_WDir/hisat2_3/hisat2_1.txt'
50 cp 'test-data/hisat2_2.txt' 'multiqc_WDir/hisat2_3/hisat2_2.txt'
51
52 mkdir 'multiqc_WDir/kallisto_4'
53 cp 'test-data/kallisto_1.txt' 'multiqc_WDir/kallisto_4/kallisto_1.txt'
54 cp 'test-data/kallisto_2.txt' 'multiqc_WDir/kallisto_4/kallisto_2.txt'
55
56 mkdir -p 'multiqc_WDir/salmon_5/fld_0/file_0'
57 cp 'test-data/salmon.txt' 'multiqc_WDir/salmon_5/fld_0/file_0/flenDist.txt'
58
59 mkdir -p 'multiqc_WDir/star_6/log_0'
60 cp 'test-data/star_log.txt' 'multiqc_WDir/star_6/log_0/star_log_Log.final.out'
61 mkdir 'multiqc_WDir/star_6/genecounts_1'
62 cp 'test-data/star_counts.txt' 'multiqc_WDir/star_6/genecounts_1/star_counts_ReadsPerGene.out.tab'
63
64 mkdir 'multiqc_WDir/tophat_7'
65 cp 'test-data/tophat.txt' 'multiqc_WDir/tophat_7/tophat_align_summary.txt'
66
67 multiqc multiqc_WDir
68
69 mv 'multiqc_report.html' 'test-data/aligner_soft_report.html'
70 mv 'multiqc_data/multiqc_bismark_alignment.txt' 'test-data/bismark_stats.tabular'
71 mv 'multiqc_data/multiqc_bowtie2.txt' 'test-data/bowtie2_stats.tabular'
72 mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/aligner_soft_stats.tabular'
73 mv 'multiqc_data/multiqc_hisat2.txt' 'test-data/hisat2_stats.tabular'
74 mv 'multiqc_data/multiqc_kallisto.txt' 'test-data/kallisto_stats.tabular'
75 mv 'multiqc_data/multiqc_star.txt' 'test-data/star_stats.tabular'
76 mv 'multiqc_data/multiqc_tophat.txt.txt' 'test-data/tophat_stats.tabular'
77
78 rm -rf 'multiqc_WDir'
79 rm -rf 'multiqc_data/'
80
81 # 3rd test
82 mkdir multiqc_WDir
83
84 mkdir 'multiqc_WDir/bamtools_0'
85 cp 'test-data/bamtools.txt' 'multiqc_WDir/bamtools_0/bamtools.txt'
86
87 mkdir 'multiqc_WDir/bcftools_1'
88 cp 'test-data/bcftools.txt' 'multiqc_WDir/bcftools_1/bcftools.txt'
89
90 mkdir 'multiqc_WDir/busco_2'
91 cp 'test-data/busco.txt' 'multiqc_WDir/busco_2/short_summary_busco.txt'
92
93 mkdir 'multiqc_WDir/featureCounts_3'
94 cp 'test-data/featureCounts.txt' 'multiqc_WDir/featureCounts_3/featureCounts.summary'
95
96 mkdir 'multiqc_WDir/gatk_4'
97 cp 'test-data/gatk_BaseRecalibrator.txt' 'multiqc_WDir/gatk_4/gatk_BaseRecalibrator.txt'
98 cp 'test-data/gatk_varianteval.txt' 'multiqc_WDir/gatk_4/gatk_varianteval.txt'
99
100 mkdir 'multiqc_WDir/htseq_5'
101 cp 'test-data/htseq.txt' 'multiqc_WDir/htseq_5/htseq.txt'
102
103 mkdir 'multiqc_WDir/picard_6'
104 cp 'test-data/picard_collectGcBias.txt' 'multiqc_WDir/picard_6/picard_collectGcBias.txt'
105 cp 'test-data/picard_CollectInsertSizeMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectInsertSizeMetrics.txt'
106 cp 'test-data/picard_MarkDuplicates.txt' 'multiqc_WDir/picard_6/picard_MarkDuplicates.txt'
107 cp 'test-data/picard_CollectBaseDistributionByCycle.txt' 'multiqc_WDir/picard_6/picard_CollectBaseDistributionByCycle.txt'
108 cp 'test-data/picard_CollectRnaSeqMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectRnaSeqMetrics.txt'
109 cp 'test-data/picard_CollectAlignmentSummaryMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectAlignmentSummaryMetrics.txt'
110
111 mkdir 'multiqc_WDir/prokka_7'
112 cp 'test-data/prokka_1.txt' 'multiqc_WDir/prokka_7/prokka_1.txt'
113 cp 'test-data/prokka_2.txt' 'multiqc_WDir/prokka_7/prokka_2.txt'
114
115 mkdir -p 'multiqc_WDir/quast_8/file_0'
116 cp 'test-data/quast.tsv' 'multiqc_WDir/quast_8/file_0/report.tsv'
117
118 #mkdir 'multiqc_WDir/rsem_9'
119 #cp 'test-data/rsem.txt' 'multiqc_WDir/rsem_9/rsem.cnt'
120
121 mkdir -p 'multiqc_WDir/rseqc_10/read_gc_0'
122 cp 'test-data/rseqc.txt' 'multiqc_WDir/rseqc_10/read_gc_0/rseq.GC.xls'
123
124 mkdir 'multiqc_WDir/samblaster_11'
125 cp 'test-data/samblaster.txt' 'multiqc_WDir/samblaster_11/samblaster.txt'
126
127 mkdir -p 'multiqc_WDir/samtools_12/stats_0'
128 cp 'test-data/samtools_stats.txt' 'multiqc_WDir/samtools_12/stats_0/samtools_stats.txt'
129 mkdir 'multiqc_WDir/samtools_12/flagstat_1'
130 cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools_12/flagstat_1/samtools_flagstat.txt'
131 mkdir 'multiqc_WDir/samtools_12/idxstats_2'
132 cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools_12/idxstats_2/samtools_idxstats_idxstat'
133
134 #mkdir 'multiqc_WDir/snpeff_13'
135 #cp 'test-data/snpeff.csv' 'multiqc_WDir/snpeff_13/snpeff.txt'
136
137 mkdir -p 'multiqc_WDir/vcftools_14/tstv_by_qual_0'
138 cp 'test-data/vcftools.txt' 'multiqc_WDir/vcftools_14/tstv_by_qual_0/vcftools.TsTv.qual'
139
140 multiqc multiqc_WDir
141
142 mv 'multiqc_report.html' 'test-data/post_aligner_soft_report.html'
143 mv 'multiqc_data/multiqc_bamtools_stats.txt' 'test-data/bamtools_stats.tabular'
144 mv 'multiqc_data/multiqc_bcftools_stats.txt' 'test-data/bcftools_stats.tabular'
145 mv 'multiqc_data/multiqc_busco.txt' 'test-data/busco_stats.tabular'
146 mv 'multiqc_data/multiqc_featureCounts.txt' 'test-data/featureCounts_stats.tabular'
147 mv 'multiqc_data/multiqc_gatk_varianteval.txt' 'test-data/gatk_varianteval_stats.tabular'
148 mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/post_aligner_soft_stats.tabular'
149 mv 'multiqc_data/multiqc_htseq.txt' 'test-data/htseq_stats.tabular'
150 mv 'multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt' 'test-data/picard_AlignmentSummaryMetrics_stats.tabular'
151 mv 'multiqc_data/multiqc_picard_RnaSeqMetrics.txt' 'test-data/picard_RnaSeqMetrics_stats.tabular'
152 mv 'multiqc_data/multiqc_picard_baseContent.txt' 'test-data/picard_baseContent_stats.tabular'
153 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'
155 mv 'multiqc_data/multiqc_prokka.txt' 'test-data/prokka_stats.tabular'
156 mv 'multiqc_data/multiqc_quast.txt' 'test-data/quast_stats.tabular'
157 #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'
160 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'
162 #mv 'multiqc_data/multiqc_snpeff.txt' 'test-data/snpeff_stats.tabular'
163
164 rm -rf 'multiqc_WDir'
165 rm -rf 'multiqc_data/'
166
167 # 4th test
168 mkdir multiqc_WDir
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'
172 cp 'test-data/cc_wt15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_1.tsv'
173
174 echo "custom_data:" > 'config_file'
175 echo " section_0:" >> 'config_file'
176 echo " file_format: 'tsv'" >> 'config_file'
177 echo " section_name: 'BPC'" >> 'config_file'
178 echo " title: 'Base peak chromatogram'" >> 'config_file'
179 echo " description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'" >> 'config_file'
180 echo " plot_type: 'linegraph'" >> 'config_file'
181 echo " pconfig:" >> 'config_file'
182 echo " id: 'section_0_linegraph'" >> 'config_file'
183 echo " ylab: 'Base Peak Intensity'" >> 'config_file'
184 echo " xlab: 'Retention Time'" >> 'config_file'
185 echo "sp:" >> 'config_file'
186 echo " section_0:" >> 'config_file'
187 echo " fn: 'file_0_*'" >> 'config_file'
188
189 multiqc multiqc_WDir -c 'config_file'
190
191 mv 'multiqc_report.html' 'test-data/report_manual_custom_content.html'
192
193 rm 'config_file'
194 rm -rf 'multiqc_WDir'
195 rm -rf 'multiqc_data/'