Mercurial > repos > iuc > multiqc

annotate generate_test_data.sh @ 12:1c2db0054039 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
author iuc
date Wed, 08 Aug 2018 08:49:39 -0400
parents df99138d2776
children
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3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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diff changeset
1 #!/usr/bin/env bash
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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3 # 1st test
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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4 mkdir -p 'multiqc_WDir/cutadapt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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5 cp 'test-data/cutadapt.txt' 'multiqc_WDir/cutadapt/cutadapt.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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6 sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt/cutadapt.txt'
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3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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7
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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8 mkdir -p 'multiqc_WDir/fastqc/data_0/file_0'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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9 cp 'test-data/fastqc_1.txt' 'multiqc_WDir/fastqc/data_0/file_0/fastqc_data.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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10 mkdir -p 'multiqc_WDir/fastqc/data_0/file_1'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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11 cp 'test-data/fastqc_2.txt' 'multiqc_WDir/fastqc/data_0/file_1/fastqc_data.txt'
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3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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12
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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13 mkdir -p 'multiqc_WDir/flexbar'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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14 cp 'test-data/flexbar.txt' 'multiqc_WDir/flexbar/flexbar.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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16 mkdir -p 'multiqc_WDir/sortmerna'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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17 cp 'test-data/sortmerna.txt' 'multiqc_WDir/sortmerna/sortmerna.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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19 mkdir -p 'multiqc_WDir/trimmomatic'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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20 cp 'test-data/trimmomatic.txt' 'multiqc_WDir/trimmomatic/trimmomatic.txt'
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3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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22 multiqc multiqc_WDir
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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24 mv 'multiqc_report.html' 'test-data/pre_alignment_soft_report.html'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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25 mv 'multiqc_data/multiqc.log' 'test-data/pre_alignment_soft_log.txt'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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26 mv 'multiqc_data/multiqc_cutadapt.txt' 'test-data/cutadapt_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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27 mv 'multiqc_data/multiqc_fastqc.txt' 'test-data/fastqc_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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28 mv 'multiqc_data/multiqc_flexbar.txt' 'test-data/flexbar_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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29 mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/pre_alignment_soft_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
30 mv 'multiqc_data/multiqc_sortmerna.txt' 'test-data/sortmerna_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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31 mv 'multiqc_data/multiqc_trimmomatic.txt' 'test-data/trimmomatic_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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33 rm -rf 'multiqc_WDir'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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34 rm -rf 'multiqc_data/'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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36 # 2nd test
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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37 mkdir -p 'multiqc_WDir/bismark'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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38 cp 'test-data/bismark.txt' 'multiqc_WDir/bismark/bismark_SE_report.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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40 mkdir -p 'multiqc_WDir/bowtie2'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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41 cp 'test-data/bowtie2_1.txt' 'multiqc_WDir/bowtie2/bowtie2_1.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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42 cp 'test-data/bowtie2_2.txt' 'multiqc_WDir/bowtie2/bowtie2_2.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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44 mkdir -p 'multiqc_WDir/hisat2'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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45 cp 'test-data/hisat2_1.txt' 'multiqc_WDir/hisat2/hisat2_1.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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46 cp 'test-data/hisat2_2.txt' 'multiqc_WDir/hisat2/hisat2_2.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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48 mkdir -p 'multiqc_WDir/hicexplorer'
9
df99138d2776 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945
iuc
parents: 8
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49 cp 'test-data/hicexplorer1.log' 'multiqc_WDir/hicexplorer/hicexplorer1'
df99138d2776 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945
iuc
parents: 8
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50 cp 'test-data/hicexplorer1.log' 'multiqc_WDir/hicexplorer/hicexplorer1_1'
df99138d2776 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945
iuc
parents: 8
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51 cp 'test-data/hicexplorer2.log' 'multiqc_WDir/hicexplorer/hicexplorer2'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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53 mkdir -p 'multiqc_WDir/kallisto'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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54 cp 'test-data/kallisto_1.txt' 'multiqc_WDir/kallisto/kallisto_1.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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55 cp 'test-data/kallisto_2.txt' 'multiqc_WDir/kallisto/kallisto_2.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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57 #mkdir -p 'multiqc_WDir/salmon/fld_0/file_0'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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58 #cp 'test-data/salmon_flenDist.txt' 'multiqc_WDir/salmon/fld_0/file_0/flenDist.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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59 #mkdir -p 'multiqc_WDir/salmon/fld_1/file_0'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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60 #cp 'test-data/salmon_meta_info.json' 'multiqc_WDir/salmon/fld_1/file_0/meta_info.json'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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62 mkdir -p 'multiqc_WDir/star/log_0'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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63 cp 'test-data/star_log.txt' 'multiqc_WDir/star/log_0/star_log_Log.final.out'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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64 mkdir -p 'multiqc_WDir/star/genecounts_1'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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65 cp 'test-data/star_counts.txt' 'multiqc_WDir/star/genecounts_1/star_counts_ReadsPerGene.out.tab'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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67 mkdir -p 'multiqc_WDir/tophat'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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68 cp 'test-data/tophat.txt' 'multiqc_WDir/tophat/tophat_align_summary.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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70 multiqc multiqc_WDir
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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72 mv 'multiqc_report.html' 'test-data/aligner_soft_report.html'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
73 mv 'multiqc_data/multiqc_bismark_alignment.txt' 'test-data/bismark_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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74 mv 'multiqc_data/multiqc_bowtie2.txt' 'test-data/bowtie2_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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75 mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/aligner_soft_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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76 mv 'multiqc_data/multiqc_hisat2.txt' 'test-data/hisat2_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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77 mv 'multiqc_data/multiqc_kallisto.txt' 'test-data/kallisto_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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78 mv 'multiqc_data/multiqc_star.txt' 'test-data/star_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
79 mv 'multiqc_data/multiqc_tophat.txt.txt' 'test-data/tophat_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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81 rm -rf 'multiqc_WDir'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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82 rm -rf 'multiqc_data/'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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83
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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84 # 3rd test
8
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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85 mkdir -p 'multiqc_WDir/bamtools'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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86 cp 'test-data/bamtools.txt' 'multiqc_WDir/bamtools/bamtools.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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87
8
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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88 mkdir -p 'multiqc_WDir/bcftools'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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89 cp 'test-data/bcftools.txt' 'multiqc_WDir/bcftools/bcftools.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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90
8
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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91 mkdir -p 'multiqc_WDir/busco'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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92 cp 'test-data/busco.txt' 'multiqc_WDir/busco/short_summary_busco.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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93
8
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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94 mkdir -p 'multiqc_WDir/deeptools'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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95 cp 'test-data/deeptools_bamPEFragmentSize.txt' 'multiqc_WDir/deeptools/'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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96 cp 'test-data/deeptools_estimateReadFiltering.txt' 'multiqc_WDir/deeptools/'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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97 cp 'test-data/deeptools_plotCoverageOutRawCounts.txt' 'multiqc_WDir/deeptools/'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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98 cp 'test-data/deeptools_plotCoverageStdout.txt' 'multiqc_WDir/deeptools/'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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99 cp 'test-data/deeptools_plotEnrichment.txt' 'multiqc_WDir/deeptools/'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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100 cp 'test-data/deeptools_plotFingerprintOutRawCounts.txt' 'multiqc_WDir/deeptools/'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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101
8
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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102 mkdir -p 'multiqc_WDir/featureCounts'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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103 cp 'test-data/featureCounts.txt' 'multiqc_WDir/featureCounts/featureCounts.summary'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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104
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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105 mkdir -p 'multiqc_WDir/gatk'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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106 cp 'test-data/gatk_BaseRecalibrator.txt' 'multiqc_WDir/gatk/gatk_BaseRecalibrator.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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107 cp 'test-data/gatk_varianteval.txt' 'multiqc_WDir/gatk/gatk_varianteval.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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108
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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109 mkdir -p 'multiqc_WDir/htseq'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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110 cp 'test-data/htseq.txt' 'multiqc_WDir/htseq/htseq.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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111
8
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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112 mkdir -p 'multiqc_WDir/picard'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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113 cp 'test-data/picard_collectGcBias.txt' 'multiqc_WDir/picard/picard_collectGcBias.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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114 cp 'test-data/picard_CollectInsertSizeMetrics.txt' 'multiqc_WDir/picard/picard_CollectInsertSizeMetrics.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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115 cp 'test-data/picard_MarkDuplicates.txt' 'multiqc_WDir/picard/picard_MarkDuplicates.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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116 cp 'test-data/picard_CollectBaseDistributionByCycle.txt' 'multiqc_WDir/picard/picard_CollectBaseDistributionByCycle.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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117 cp 'test-data/picard_CollectRnaSeqMetrics.txt' 'multiqc_WDir/picard/picard_CollectRnaSeqMetrics.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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118 cp 'test-data/picard_CollectAlignmentSummaryMetrics.txt' 'multiqc_WDir/picard/picard_CollectAlignmentSummaryMetrics.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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119
8
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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120 mkdir -p 'multiqc_WDir/prokka'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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121 cp 'test-data/prokka_1.txt' 'multiqc_WDir/prokka/prokka_1.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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122 cp 'test-data/prokka_2.txt' 'multiqc_WDir/prokka/prokka_2.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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123
8
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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124 mkdir -p 'multiqc_WDir/quast/file_0'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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125 cp 'test-data/quast.tsv' 'multiqc_WDir/quast/file_0/report.tsv'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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126
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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127 #mkdir -p 'multiqc_WDir/rsem'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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128 #cp 'test-data/rsem.txt' 'multiqc_WDir/rsem/rsem.cnt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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129
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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130 mkdir -p 'multiqc_WDir/rseqc/read_gc_0'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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131 cp 'test-data/rseqc.txt' 'multiqc_WDir/rseqc/read_gc_0/rseq.GC.xls'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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132
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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133 mkdir -p 'multiqc_WDir/samblaster'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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134 cp 'test-data/samblaster.txt' 'multiqc_WDir/samblaster/samblaster.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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135
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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136 mkdir -p 'multiqc_WDir/samtools/stats_0'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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137 cp 'test-data/samtools_stats.txt' 'multiqc_WDir/samtools/stats_0/samtools_stats.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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138 mkdir -p 'multiqc_WDir/samtools/flagstat_1'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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139 cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools/flagstat_1/samtools_flagstat.txt'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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140 mkdir -p 'multiqc_WDir/samtools/idxstats_2'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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141 cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools/idxstats_2/samtools_idxstats_idxstat'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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142
8
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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143 mkdir -p 'multiqc_WDir/snpeff'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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144 cp 'test-data/snpeff.csv' 'multiqc_WDir/snpeff/snpeff.txt'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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145
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
parents: 0
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146 mkdir -p 'multiqc_WDir/vcftools/tstv_by_qual_0'
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
iuc
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147 cp 'test-data/vcftools.txt' 'multiqc_WDir/vcftools/tstv_by_qual_0/vcftools.TsTv.qual'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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148
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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149 multiqc multiqc_WDir
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
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150
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
151 mv 'multiqc_report.html' 'test-data/post_aligner_soft_report.html'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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152 mv 'multiqc_data/multiqc_bamtools_stats.txt' 'test-data/bamtools_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
153 mv 'multiqc_data/multiqc_bcftools_stats.txt' 'test-data/bcftools_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
154 mv 'multiqc_data/multiqc_busco.txt' 'test-data/busco_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
155 mv 'multiqc_data/multiqc_featureCounts.txt' 'test-data/featureCounts_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
156 mv 'multiqc_data/multiqc_gatk_varianteval.txt' 'test-data/gatk_varianteval_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
157 mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/post_aligner_soft_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
158 mv 'multiqc_data/multiqc_htseq.txt' 'test-data/htseq_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
159 mv 'multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt' 'test-data/picard_AlignmentSummaryMetrics_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
160 mv 'multiqc_data/multiqc_picard_RnaSeqMetrics.txt' 'test-data/picard_RnaSeqMetrics_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
161 mv 'multiqc_data/multiqc_picard_baseContent.txt' 'test-data/picard_baseContent_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
diff changeset
162 mv 'multiqc_data/multiqc_picard_dups.txt' 'test-data/picard_dups_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
iuc
parents:
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163 mv 'multiqc_data/multiqc_picard_insertSize.txt' 'test-data/picard_insertSize_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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164 mv 'multiqc_data/multiqc_prokka.txt' 'test-data/prokka_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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165 mv 'multiqc_data/multiqc_quast.txt' 'test-data/quast_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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166 #mv 'multiqc_data/multiqc_rsem.txt' 'test-data/rsem_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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167 mv 'multiqc_data/multiqc_samblaster.txt' 'test-data/samblaster_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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168 mv 'multiqc_data/multiqc_samtools_flagstat.txt' 'test-data/samtools_flagstat_stats.tabular'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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169 mv 'multiqc_data/multiqc_samtools_stats.txt' 'test-data/samtools_stats_stats.tabular'
8
e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
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170 mv 'multiqc_data/multiqc_snpeff.txt' 'test-data/snpeff_stats.tabular'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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171
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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172 rm -rf 'multiqc_WDir'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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173 rm -rf 'multiqc_data/'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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174
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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175 # 4th test
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e0f4a651c6b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
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176 mkdir -p 'multiqc_WDir/custom_content_0'
0
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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177 cp 'test-data/cc_ko15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_0.tsv'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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178 cp 'test-data/cc_wt15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_1.tsv'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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179
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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180 echo "custom_data:" > 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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181 echo " section_0:" >> 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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182 echo " file_format: 'tsv'" >> 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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183 echo " section_name: 'BPC'" >> 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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184 echo " title: 'Base peak chromatogram'" >> 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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185 echo " description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'" >> 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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186 echo " plot_type: 'linegraph'" >> 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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187 echo " pconfig:" >> 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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188 echo " id: 'section_0_linegraph'" >> 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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189 echo " ylab: 'Base Peak Intensity'" >> 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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190 echo " xlab: 'Retention Time'" >> 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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191 echo "sp:" >> 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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192 echo " section_0:" >> 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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193 echo " fn: 'file_0_*'" >> 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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194
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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195 multiqc multiqc_WDir -c 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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196
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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197 mv 'multiqc_report.html' 'test-data/report_manual_custom_content.html'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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198
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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199 rm 'config_file'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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200 rm -rf 'multiqc_WDir'
3bad335ccea9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306
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201 rm -rf 'multiqc_data/'