Mercurial > repos > public-health-bioinformatics > fastp_json_to_tabular

annotate fastp_json_to_tabular.py @ 2:2c2d59b3d64d draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit 225d05a1238c15522c9bc3b47fcc6c0bbe2e7b50-dirty"
author public-health-bioinformatics
date Thu, 10 Mar 2022 00:13:02 +0000
parents dc655c5e77d6
children e342bf27e717
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dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
parents:
diff changeset
1 #!/usr/bin/env python
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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2
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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3 import argparse
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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4 import json
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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5
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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6 def main(args):
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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7 with open(args.fastp_json, 'r') as f:
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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8 fastp_report = json.load(f)
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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9
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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10 total_reads_before_filtering = fastp_report['summary']['before_filtering']['total_reads']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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11 total_reads_after_filtering = fastp_report['summary']['after_filtering']['total_reads']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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12 total_bases_before_filtering = fastp_report['summary']['before_filtering']['total_bases']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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13 total_bases_after_filtering = fastp_report['summary']['after_filtering']['total_bases']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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14 read1_mean_length_before_filtering = fastp_report['summary']['before_filtering']['read1_mean_length']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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15 read2_mean_length_before_filtering = fastp_report['summary']['before_filtering']['read2_mean_length']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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16 read1_mean_length_after_filtering = fastp_report['summary']['after_filtering']['read1_mean_length']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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17 read2_mean_length_after_filtering = fastp_report['summary']['after_filtering']['read2_mean_length']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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18 q20_bases_before_filtering = fastp_report['summary']['before_filtering']['q20_bases']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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19 q20_bases_after_filtering = fastp_report['summary']['after_filtering']['q20_bases']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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20 q20_rate_before_filtering = fastp_report['summary']['before_filtering']['q20_rate']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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21 q20_rate_after_filtering = fastp_report['summary']['after_filtering']['q20_rate']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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22 q30_bases_before_filtering = fastp_report['summary']['before_filtering']['q30_bases']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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23 q30_bases_after_filtering = fastp_report['summary']['after_filtering']['q30_bases']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
parents:
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24 q30_rate_before_filtering = fastp_report['summary']['before_filtering']['q30_rate']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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25 q30_rate_after_filtering = fastp_report['summary']['after_filtering']['q30_rate']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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26 gc_content_before_filtering = fastp_report['summary']['before_filtering']['gc_content']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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27 gc_content_after_filtering = fastp_report['summary']['after_filtering']['gc_content']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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28 adapter_trimmed_reads = fastp_report['adapter_cutting']['adapter_trimmed_reads']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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29 adapter_trimmed_bases = fastp_report['adapter_cutting']['adapter_trimmed_bases']
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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30
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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31
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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32 output_fields = [
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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33 'total_reads_before_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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34 'total_reads_after_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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35 'total_bases_before_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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36 'total_bases_after_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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37 'read1_mean_length_before_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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38 'read1_mean_length_after_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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39 'read2_mean_length_before_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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40 'read2_mean_length_after_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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41 'q20_bases_before_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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42 'q20_bases_after_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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43 'q20_rate_before_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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44 'q20_rate_after_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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45 'q30_bases_before_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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46 'q30_bases_after_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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47 'q30_rate_before_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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48 'q30_rate_after_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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49 'gc_content_before_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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50 'gc_content_after_filtering',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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51 'adapter_trimmed_reads',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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52 'adapter_trimmed_bases',
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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53 ]
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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54
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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55 output_data = []
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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56 if args.sample_id:
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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57 output_fields = ['sample_id'] + output_fields
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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58 output_data = [args.sample_id]
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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59
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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60 print(args.delimiter.join(output_fields))
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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61
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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62 output_data = output_data + [
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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63 total_reads_before_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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64 total_reads_after_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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65 total_bases_before_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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66 total_bases_after_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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67 read1_mean_length_before_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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68 read1_mean_length_after_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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69 read2_mean_length_before_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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70 read2_mean_length_after_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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71 q20_bases_before_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
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72 q20_bases_after_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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73 q20_rate_before_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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74 q20_rate_after_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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diff changeset
75 q30_bases_before_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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76 q30_bases_after_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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diff changeset
77 q30_rate_before_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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78 q30_rate_after_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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79 gc_content_before_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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diff changeset
80 gc_content_after_filtering,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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diff changeset
81 adapter_trimmed_reads,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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82 adapter_trimmed_bases,
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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83 ]
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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84 print(args.delimiter.join(map(str, output_data)))
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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85
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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86
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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87 if __name__ == "__main__":
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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88 parser = argparse.ArgumentParser()
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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89 parser.add_argument('fastp_json')
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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90 parser.add_argument('-s', '--sample-id')
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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91 parser.add_argument('-d', '--delimiter', default='\t')
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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92 args = parser.parse_args()
dc655c5e77d6 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit c6ac9f7bd10c58d2b4168cab62b812d4d76283fe"
public-health-bioinformatics
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93 main(args)