Mercurial > repos > iuc > pycoqc

annotate pycoqc.xml @ 1:3a2f2e24c37e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 3e30ad2c5cdb20dcb12d4ca2747f93fcd57b67b0"
author iuc
date Thu, 11 Mar 2021 16:25:17 +0000
parents 6fd0573c0e93
children dc1500f42073
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rev   line source
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6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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1 <?xml version="1.0"?>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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2 <tool id="pycoqc" name="Pycoqc" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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3 <description></description>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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4 <macros>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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5 <import>macros.xml</import>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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6 </macros>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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7 <expand macro="requirements"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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8
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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9 <expand macro="version_command"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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10
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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11 <command detect_errors="exit_code"><![CDATA[
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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12 pycoQC
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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13 --min_pass_qual '$min_pass_qual'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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14 --min_pass_len '$min_pass_len'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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15 #if $filter_calibration:
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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16 '$filter_calibration'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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17 #end if
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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18 #if $filter_duplicated:
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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19 '$filter_duplicated'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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20 #end if
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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21 --min_barcode_percent '$min_barcode_percent'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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22 --report_title '$report_title'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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23 ## TODO in future - --template_file
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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24 ## TODO in future - --config_file
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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25 #if $skip_coverage_plot
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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26 '$skip_coverage_plot'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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27 #end if
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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28 --sample '$sample'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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29 ## TODO in future --default_config
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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30 --summary_file '$summary_file'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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31 ## TODO in future --barcode_file
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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32 #if $bam_file:
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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33 --bam_file '$bam_file'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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34 #end if
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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35 --html_outfile '$out_html'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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36 #if $out_json:
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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37 --json_outfile '$out_json'
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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38 #end if
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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39 ]]></command>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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40 <inputs>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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41 <param argument="--summary_file" type="data" format="txt,tabular" label="A sequencing_summary file" help="Must be generated by Albacore 1.0.0 + (read_fast5_basecaller.py) / Guppy 2.1.3+ (guppy_basecaller)" />
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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42 <!-- <param argument="barcode_file" type="data" format="txt" label="" /> -->
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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43 <param argument="--bam_file" type="data" format="bam" label="An alignment file generated by aligning the reads described in the sequencing_summary file" optional="true"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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44 <param name="output_json_bool" type="boolean" checked="true" label="Output JSON Summary File?"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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45 <param argument="--min_pass_qual" type="integer" value="7" min="0" label="Minimum quality to consider a read as 'pass'" />
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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46 <param argument="--min_pass_len" type="integer" value="0" min="0" label="Minimum read length to consider a read as 'pass'"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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47 <param argument="--filter_calibration" type="boolean" checked="false" truevalue="--filter_calibration" falsevalue="" label="Filter Calibration?" help="If yes, reads flagged as calibration strand by the basecaller are removed" />
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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48 <param argument="--filter_duplicated" type="boolean" checked="false" truevalue="--filter_duplicated" falsevalue="" label="Filter Duplicated?" help="If yes, duplicated read_ids are removed but the first occurence is kept (Guppy sometimes outputs the same read multiple times)" />
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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49 <param argument="--min_barcode_percent" type="float" value="0.1" label="Minimal percent of total reads to retain barcode label" help="If below, the barcode value is set as unclassified" />
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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50 <param argument="--report_title" type="text" value="PycoQC report" label="Title to use in the html report" />
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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51 <param argument="--skip_coverage_plot" type="boolean" checked="false" truevalue="--skip_coverage_plot" falsevalue="" label="Skip the coverage plot in HTML report?" help="Useful when using a reference file containing many sequences, i.e. transcriptome" />
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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52 <param argument="--sample" type="integer" label="Number of reads will be randomly selected instead of the entire dataset for ploting function" help="(deterministic sampling)" value="100000"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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53 </inputs>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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54 <outputs>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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55 <!-- standard -->
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56 <data name="out_html" format="html" label="${tool.name} on ${on_string}: HTML Report"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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57 <data name="out_json" format="json" label="${tool.name} on ${on_string}: JSON Summary">
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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58 <filter>output_json_bool</filter>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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59 </data>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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60 </outputs>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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61 <tests>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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62 <!-- #1 default -->
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63 <test expect_num_outputs="2">
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64 <param name="summary_file" value="test.txt"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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65 <output name="out_html">
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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66 <assert_contents>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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67 <has_line line="&lt;!doctype html&gt;"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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68 <has_n_lines n="300"/>
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69 </assert_contents>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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70 </output>
1
3a2f2e24c37e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 3e30ad2c5cdb20dcb12d4ca2747f93fcd57b67b0"
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71 <output name="out_json" file="test.json" lines_diff="2"/>
0
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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72 </test>
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73 </tests>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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74 <help><![CDATA[
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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75 .. class:: infomark
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76
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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77 **What it does**
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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78
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79 @WID@
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80
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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81 **Input**
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82
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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83 - Guppy Sequencing Summary Output (tsv)
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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84 - Aligned Reads (bam) (Optional)
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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85
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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86 **Output**
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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87
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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88 - Output QC Report (HTML)
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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89 - Output QC Metrics (JSON)
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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90
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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91
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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92 **References**
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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93
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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94 @REFERENCES@
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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95 ]]></help>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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96 <expand macro="citations"/>
6fd0573c0e93 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
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97 </tool>