Mercurial > repos > iuc > mykrobe_predict

annotate mykrobe_predict.xml @ 2:cedd631dc124 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 65f9e423263afc8f23fa51cb4770998b99f933ba"
author iuc
date Thu, 02 Jan 2020 12:03:50 -0500
parents 60ffb465aa4d
children e8405163fb4e
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cedd631dc124 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 65f9e423263afc8f23fa51cb4770998b99f933ba"
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1 <tool id="mykrobe_predict" name="mkyrobe predict" version="0.7.0">
0
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2 <description>Antibiotic resistance predictions</description>
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3 <macros>
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4 <import>macro.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
1
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9 @select_inputs@
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10
1
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11 mykrobe predict
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12 '${name}'
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13 ${select_species.species}
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14
1
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15 #if $select_species.panel == 'custom':
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16 #if $adv.custom_probe:
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17 --custom_probe_set_path '${adv.custom_probe}'
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18 #end if
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19 #if $adv.custom_variant_to_resistance:
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20 --custom_variant_to_resistance_json '${adv.custom_variant_to_resistance}'
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21 #end if
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22 #elif $select_species.panel:
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23 --panel '${select_species.panel}'
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24 #end if
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25
1
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26 #if $conf_percent_cutoff:
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27 --conf_percent_cutoff '${conf_percent_cutoff}'
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28 #end if
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29
1
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30 #if $min_depth:
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31 --min_depth '${min_depth}'
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32 #end if
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33
1
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34 @shared_options@
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35
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36 -q
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37 -t "\${GALAXY_SLOTS:-1}"
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38
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39 -1
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40 #if $type == 'fastq':
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41 *.fastq
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42 #else
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43 *.bam
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44 #end if
1
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45
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46 --format '${format}'
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47
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48 > '$output'
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49 ]]>
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50 </command>
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51 <inputs>
1
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52 <expand macro="inputs"/>
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53 <conditional name="select_species">
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54 <param name="species" type="select" label="Specify Species for AMR">
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55 <option value="tb">Mycobacterium tuberculosis (tb)</option>
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56 <option value="staph">Staphylococcus aureus (staph)</option>
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57 </param>
1
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58 <when value="staph">
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59 <param name="panel" type="select" optional="true" label="Select panel for Staph only">
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60 <option value="custom">Custom</option>
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61 </param>
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62 </when>
0
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63 <when value="tb">
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64 <param name="panel" type="select" label="Select panel for TB only">
1
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65 <option value="201901">201901</option>
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66 <option value="bradley-2015">Bradely 2015</option>
1
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67 <option value="walker-2015">Walker 2015</option>
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68 <option value="custom">Custom</option>
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69 </param>
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70 </when>
1
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71 </conditional>
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72 <section name="adv" title="Custom Panel" expanded="false">
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73 <param name="custom_probe" type="data" format="fasta" label="Custom Probe" optional="True" help="Don't include filtered genotypes"/>
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74 <param name="custom_variant_to_resistance" type="data" format="json" label="Custom Variant to Resistance" optional="True" help="JSON file with key,value pairs of variant names and induced drug resistance."/>
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75 </section>
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76 <param argument="--min_depth" optional="True" type="integer" min="0" label="Minimum depth" help=""/>
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77 <param argument="--conf_percent_cutoff" optional="True" type="integer" label="Confidence percent cutoff" help="Number between 0 and 100. Determines --min_variant_conf, by simulating variants and choosing the cutoff that would keep x% of the variants. Default is 90 if --ont, otherwise --min_variant_conf is used as the cutoff">
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78 <validator type="in_range" min="0" max="100" message="Confidence percent cutoff should be between 0 and 100" />
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79 </param>
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80 <expand macro="options"/>
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81 <param argument="--format" type="select" label="Select the prefered output format">
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82 <option value="csv" >csv</option>
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83 <option value="json">json</option>
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84 </param>
0
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85 </inputs>
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86 <outputs>
1
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87 <data name="output" format="csv" label="prediction">
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88 <change_format>
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89 <when input="format" value="json" format="json"/>
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90 </change_format>
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91 </data>
0
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92 </outputs>
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93 <tests>
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94 <test>
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95 <param name="type" value="single"/>
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96 <param name="fastq_input1" value="reads.fastq"/>
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97 <param name="species" value="tb"/>
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98 <param name="panel" value="bradley-2015"/>
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99 <param name="format" value="json"/>
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100 <output name="output">
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101 <assert_contents>
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102 <has_text_matching expression="susceptibility"/>
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103 </assert_contents>
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104 </output>
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105 </test>
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106 </tests>
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107 <help>
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108 @ATTRIBUTION@
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109 </help>
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110 <expand macro="citation" />
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111 </tool>