Mercurial > repos > sanbi-uwc > qc
changeset 6:878f18249f76 draft
"planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/qc commit 21d348651ca466563cc507b9e3a3fbd6c2b0a016"
| author | sanbi-uwc |
|---|---|
| date | Mon, 12 Apr 2021 12:28:41 +0000 |
| parents | 499b71c93c5d |
| children | 6bdec8c62aec |
| files | qc.py qc.xml |
| diffstat | 2 files changed, 14 insertions(+), 5 deletions(-) [+] |
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--- a/qc.py Wed Apr 07 22:07:00 2021 +0000 +++ b/qc.py Mon Apr 12 12:28:41 2021 +0000 @@ -6,6 +6,7 @@ import pandas as pd import matplotlib.pyplot as plt import shlex +import json """ This script can incorporate as many QC checks as required @@ -156,7 +157,12 @@ writer = csv.DictWriter(csvfile, fieldnames=header) writer.writeheader() writer.writerow(qc_line) - + + # write a json file from the dict + json_file = args.outfile + '.json' + with open(args.outfile, 'w') as jsonfile: + json.dump(qc_line, json_file) + N_density = sliding_window_N_density(fasta) make_qc_plot(depth_pos, N_density, args.sample)
--- a/qc.xml Wed Apr 07 22:07:00 2021 +0000 +++ b/qc.xml Mon Apr 12 12:28:41 2021 +0000 @@ -11,8 +11,9 @@ --sample 'sample' --ref '$input_ref' --bam '$input_bam' - --fasta '$input_cons_fasta' && - mv sample.depth.png '$output2' + --fasta '$input_cons_fasta' && + mv '$output1'.json '$output2' && + mv sample.depth.png '$output3' ]]></command> <inputs> <conditional name="qc_type_conditional"> @@ -27,7 +28,8 @@ </inputs> <outputs> <data name="output1" format="csv" label="${tool.name} on ${on_string}: tubular output"/> - <data name="output2" format="png" label="${tool.name} on ${on_string}: depth and density"/> + <data name="output2" format="json" label="${tool.name} on ${on_string}: json output"/> + <data name="output3" format="png" label="${tool.name} on ${on_string}: depth and density"/> </outputs> <tests> <test> @@ -36,7 +38,8 @@ <param name="input_bam" value="sample.bam"/> <param name="input_cons_fasta" value="sample_consensus.fasta"/> <output name="output1" file="test_sample.qc.csv"/> - <output name="output2" file="test_sample.depth.png"/> + <output name="output2" file="test_sample.qc.json"/> + <output name="output3" file="test_sample.depth.png"/> </test> </tests> <help><![CDATA[