Mercurial > repos > public-health-bioinformatics > fastp_json_to_tabular

annotate fastp_json_to_tabular.py @ 4:b86961fa4ac4 draft default tip

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit 0cedf8014d943912974969f1ed294f6d0ec8f258"
author public-health-bioinformatics
date Thu, 10 Mar 2022 19:14:05 +0000
parents e342bf27e717
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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
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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"
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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"
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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"
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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"
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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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e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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10 reads_single_paired = fastp_report['summary']['sequencing'].split(' ')[0]
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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12 if reads_single_paired == 'paired':
4
b86961fa4ac4 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit 0cedf8014d943912974969f1ed294f6d0ec8f258"
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13 total_read_pairs_before_filtering = str(int(int(fastp_report['summary']['before_filtering']['total_reads']) / 2))
b86961fa4ac4 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit 0cedf8014d943912974969f1ed294f6d0ec8f258"
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14 total_read_pairs_after_filtering = str(int(int(fastp_report['summary']['after_filtering']['total_reads']) / 2))
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e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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15 read2_mean_length_before_filtering = fastp_report['summary']['before_filtering']['read2_mean_length']
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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16 read2_mean_length_after_filtering = fastp_report['summary']['after_filtering']['read2_mean_length']
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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17 else:
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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18 total_read_pairs_before_filtering = 'NA'
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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19 total_read_pairs_after_filtering = 'NA'
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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20 read2_mean_length_before_filtering = 'NA'
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
public-health-bioinformatics
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21 read2_mean_length_after_filtering = 'NA'
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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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
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23 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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24 total_reads_after_filtering = fastp_report['summary']['after_filtering']['total_reads']
3
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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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
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26 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"
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27 total_bases_after_filtering = fastp_report['summary']['after_filtering']['total_bases']
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e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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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
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29 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"
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30 read1_mean_length_after_filtering = fastp_report['summary']['after_filtering']['read1_mean_length']
3
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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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
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32 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"
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33 q20_bases_after_filtering = fastp_report['summary']['after_filtering']['q20_bases']
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e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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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
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35 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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36 q20_rate_after_filtering = fastp_report['summary']['after_filtering']['q20_rate']
3
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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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"
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38 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"
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39 q30_bases_after_filtering = fastp_report['summary']['after_filtering']['q30_bases']
3
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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0
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 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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42 q30_rate_after_filtering = fastp_report['summary']['after_filtering']['q30_rate']
3
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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0
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 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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45 gc_content_after_filtering = fastp_report['summary']['after_filtering']['gc_content']
3
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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46 if 'adapter_cutting' in fastp_report:
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
public-health-bioinformatics
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47 adapter_trimmed_reads = fastp_report['adapter_cutting']['adapter_trimmed_reads']
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
public-health-bioinformatics
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48 adapter_trimmed_bases = fastp_report['adapter_cutting']['adapter_trimmed_bases']
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
public-health-bioinformatics
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49 else:
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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50 adapter_trimmed_reads = 0
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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51 adapter_trimmed_bases = 0
0
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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52
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 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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54 'total_reads_before_filtering',
3
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
public-health-bioinformatics
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55 'total_read_pairs_before_filtering',
0
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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56 'total_reads_after_filtering',
3
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
public-health-bioinformatics
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57 'total_read_pairs_after_filtering',
0
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 '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"
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59 '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"
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60 '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"
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61 '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"
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62 '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"
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63 '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"
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64 '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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65 '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"
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66 '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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67 '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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68 '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"
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69 '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"
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70 '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"
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71 '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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72 '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"
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73 '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"
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74 '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"
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75 '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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76 ]
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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77
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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78 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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79 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"
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80 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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81 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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82
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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83 print(args.delimiter.join(output_fields))
3
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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84
0
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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85 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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86 total_reads_before_filtering,
3
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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87 total_read_pairs_before_filtering,
0
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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88 total_reads_after_filtering,
3
e342bf27e717 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit fb12c97e94741abedc71332572bdcb33338504a7"
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89 total_read_pairs_after_filtering,
0
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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90 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"
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91 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"
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92 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"
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93 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"
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94 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"
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95 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"
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96 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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97 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"
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98 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"
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99 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"
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100 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"
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101 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"
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102 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"
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103 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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104 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"
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105 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"
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106 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"
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107 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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108 ]
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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109 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"
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110
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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111
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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112 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"
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113 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"
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114 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"
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115 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"
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116 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"
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117 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"
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118 main(args)