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comparison mykrobe_parser.xml @ 6:8e7e5a660942 draft

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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
author nml
date Fri, 22 Sep 2023 17:24:02 +0000
parents deebc6410d13
children 12b397ad8687
comparison
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5:deebc6410d13 6:8e7e5a660942
1 <tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.4.1"> 1 <tool id="mykrobe_parseR" name="mykrobe_parseR" version="@VERSION@+galaxy1" profile="16.04">
2 <macros>
3 <token name="@VERSION@">0.1.4.1</token>
4 </macros>
2 <requirements> 5 <requirements>
3 <requirement type="package" version="3.4.1">r-base</requirement> 6 <requirement type="package" version="3.4.1">r-base</requirement>
4 <requirement type="package" version="1.5.0">r-jsonlite</requirement> 7 <requirement type="package" version="1.5.0">r-jsonlite</requirement>
5 <requirement type="package" version="0.1.0">r-here</requirement> 8 <requirement type="package" version="0.1.0">r-here</requirement>
6 <requirement type="package" version="0.7.6">r-dplyr</requirement> 9 <requirement type="package" version="0.7.6">r-dplyr</requirement>
28 -D "$depth" 31 -D "$depth"
29 #end if 32 #end if
30 #if $confidence 33 #if $confidence
31 -c "$confidence" 34 -c "$confidence"
32 #end if 35 #end if
36 #if $panel
37 -p "$panel"
38 #end if
33 #if $run_name 39 #if $run_name
34 -n "$run_name" 40 -n "$run_name"
35 #end if 41 #end if
36 42
37 ]]></command> 43 ]]></command>
40 type="data" format="json,txt" 46 type="data" format="json,txt"
41 optional="false" 47 optional="false"
42 multiple="true" 48 multiple="true"
43 label="JSON File(s) (.JSON or .TXT)"/> 49 label="JSON File(s) (.JSON or .TXT)"/>
44 <param name="version" type="text" 50 <param name="version" type="text"
45 argument="-v" 51 argument="-v"
46 optional="true" 52 optional="true"
47 label="Mykrobe Workflow Version"/> 53 label="Mykrobe Workflow Version"/>
54 <param name="panel" type="select" label="Mykrobe Panel Version" multiple="false">
55 <option value="2019">2019</option>
56 <option value="2020">2020</option>
57 </param>
48 <param name="depth" type="integer" 58 <param name="depth" type="integer"
49 argument="-D" 59 argument="-D"
50 optional="true" 60 optional="true"
51 label="Minimum depth of coverage" 61 label="Minimum depth of coverage"
52 help="Enter integer values only. Default is 5"/> 62 help="Enter integer values only. Default is 5"/>
59 argument="-n" 69 argument="-n"
60 optional="true" 70 optional="true"
61 label="Name of Run"/> 71 label="Name of Run"/>
62 </inputs> 72 </inputs>
63 <outputs> 73 <outputs>
64 <data name="output-jsondata" from_work_dir="output-jsondata.csv" format="csv" label="jsondata"/> 74 <data name="output_jsondata" from_work_dir="output-jsondata.csv" format="csv" label="jsondata"/>
65 <data name="output-report" from_work_dir="output-report.csv" format="csv" label="report"/> 75 <data name="output_report" from_work_dir="output-report.csv" format="csv" label="report"/>
66 </outputs> 76 </outputs>
67 <tests> 77 <tests>
68 <test> 78 <test>
69 <param name="input" value="test-data.json"/> 79 <param name="input" value="prediction_2019/data/ERR031480_L6.json,prediction_2019/data/ERR125628_MBOV.json,prediction_2019/data/ERR181314_L9.json,prediction_2019/data/ERR234162_L3.json,prediction_2019/data/ERR2659153.json,prediction_2019/data/ERR266106_MCAN.json,prediction_2019/data/ERR2704812_L5.json,prediction_2019/data/ERR3335753_L1.json,prediction_2019/data/ERR4143897_MPIN.json,prediction_2019/data/ERR756348_L7.json,prediction_2019/data/ERR841495_L5.json,prediction_2019/data/SRR17089001.json,prediction_2019/data/SRR1710097_L2.json,prediction_2019/data/SRR3500411_MMUN.json,prediction_2019/data/SRR9157804.json"/>
70 <output name="output-jsondata" ftype="csv" value="output-jsondata.csv" compare="sim_size"/> 80 <param name="panel" value="2019"/>
71 <output name="output-report" ftype="csv" value="output-report.csv" compare="sim_size"/> 81 <output name="output_jsondata" ftype="csv" value="prediction_2019/output-jsondata.csv"/>
82 <output name="output_report" ftype="csv" value="prediction_2019/output-report.csv"/>
83 </test>
84 <test>
85 <param name="input" value="prediction_2020/data/ERR031480_L6.json,prediction_2020/data/ERR125628_MBOV.json,prediction_2020/data/ERR181314_L9.json,prediction_2020/data/ERR234162_L3.json,prediction_2020/data/ERR2659153.json,prediction_2020/data/ERR266106_MCAN.json,prediction_2020/data/ERR2704812_L5.json,prediction_2020/data/ERR3335753_L1.json,prediction_2020/data/ERR4143897_MPIN.json,prediction_2020/data/ERR756348_L7.json,prediction_2020/data/ERR841495_L5.json,prediction_2020/data/SRR17089001.json,prediction_2020/data/SRR1710097_L2.json,prediction_2020/data/SRR3500411_MMUN.json,prediction_2020/data/SRR9157804.json"/>
86 <param name="panel" value="2020"/>
87 <output name="output_jsondata" ftype="csv" value="prediction_2020/output-jsondata.csv"/>
88 <output name="output_report" ftype="csv" value="prediction_2020/output-report.csv"/>
89 </test>
90 <test>
91 <param name="input" value="single_2019/single2019.json"/>
92 <param name="panel" value="2019"/>
93 <output name="output_jsondata" ftype="csv" value="single_2019/output-jsondata.csv"/>
94 <output name="output_report" ftype="csv" value="single_2019/output-report.csv"/>
95 </test>
96 <test>
97 <param name="input" value="single_2020/single2020.json"/>
98 <param name="panel" value="2020"/>
99 <output name="output_jsondata" ftype="csv" value="single_2020/output-jsondata.csv"/>
100 <output name="output_report" ftype="csv" value="single_2020/output-report.csv"/>
72 </test> 101 </test>
73 </tests> 102 </tests>
74 <help><![CDATA[ 103 <help><![CDATA[
75 ============== 104 ==============
76 Mykrobe Parser 105 Mykrobe Parser