Mercurial > repos > iuc > multiqc
comparison generate_test_data.sh @ 8:e0f4a651c6b9 draft
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 |
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| 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' |