Mercurial > repos > iuc > mykrobe_predict

annotate mykrobe_predict.xml @ 3:e8405163fb4e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
author iuc
date Tue, 10 Aug 2021 11:29:58 +0000
parents cedd631dc124
children a2e3ad69ee23
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3
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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1 <tool id="mykrobe_predict" name="mkyrobe predict" version="@TOOL_VERSION@">
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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 --sample '${name}'
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13 --species ${select_species.species}
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14 --panel '${select_species.panel}'
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1
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16 #if $conf_percent_cutoff:
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17 --conf_percent_cutoff '${conf_percent_cutoff}'
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18 #end if
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19
1
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20 #if $min_depth:
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21 --min_depth '${min_depth}'
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22 #end if
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23
1
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24 @shared_options@
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26 -q
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27 -t "\${GALAXY_SLOTS:-1}"
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28
3
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29 --seq
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30 #if $data_type.type == "single":
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31 $data_type.seq1
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32 #elif $data_type.type == "paired":
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33 $data_type.seq1 $data_type.seq2
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34 #elif $data_type.type == "collection":
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35 $data_type.collection1.forward $data_type.collection1.reverse
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36 #end if
1
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37
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38 --format '${format}'
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39
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40 > '$output'
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41 ]]>
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42 </command>
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43 <inputs>
1
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44 <expand macro="inputs"/>
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45 <conditional name="select_species">
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46 <param name="species" type="select" label="Specify Species for AMR">
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47 <option value="tb">Mycobacterium tuberculosis (tb)</option>
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48 <option value="staph">Staphylococcus aureus (staph)</option>
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49 <option value="sonnei">Shigella sonnei (sonnei)</option>
0
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50 </param>
1
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51 <when value="staph">
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52 <param name="panel" type="select" label="Select panel for Staph only">
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53 <option value="20170217">20170217</option>
1
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54 </param>
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55 </when>
0
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56 <when value="tb">
3
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57 <param name="panel" type="select" label="Select panel for TB only">
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58 <option value="202010">202010</option>
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59 <option value="201901">201901</option>
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60 <option value="bradley-2015">Bradely 2015</option>
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61 </param>
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62 </when>
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63 <when value="sonnei">
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64 <param name="panel" type="select" label="Select panel for sonnei only">
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65 <option value="20210201">20210201</option>
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66 <option value="20201012">20201012</option>
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67 </param>
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68 </when>
1
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69 </conditional>
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70 <param argument="--min_depth" optional="True" type="integer" min="0" label="Minimum depth" help=""/>
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71 <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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72 <validator type="in_range" min="0" max="100" message="Confidence percent cutoff should be between 0 and 100" />
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73 </param>
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74 <expand macro="options"/>
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75 <param argument="--format" type="select" label="Select the prefered output format">
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76 <option value="csv" >csv</option>
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77 <option value="json">json</option>
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78 </param>
0
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79 </inputs>
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80 <outputs>
1
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81 <data name="output" format="csv" label="prediction">
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82 <change_format>
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83 <when input="format" value="json" format="json"/>
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84 </change_format>
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85 </data>
0
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86 </outputs>
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87 <tests>
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88 <test>
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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89 <param name="type" value="single"/>
3
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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90 <param name="seq1" ftype="fastq" value="reads.fastq"/>
0
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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91 <param name="species" value="tb"/>
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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92 <param name="panel" value="bradley-2015"/>
1
60ffb465aa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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93 <param name="format" value="json"/>
60ffb465aa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
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94 <output name="output">
0
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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95 <assert_contents>
1
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96 <has_text_matching expression="susceptibility"/>
0
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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97 </assert_contents>
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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98 </output>
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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99 </test>
3
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100 <test>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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101 <param name="type" value="single"/>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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102 <param name="seq1" ftype="fastq" value="reads.fastq"/>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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103 <param name="species" value="sonnei"/>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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104 <param name="panel" value="20201012"/>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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105 <param name="format" value="json"/>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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106 <output name="output">
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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107 <assert_contents>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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108 <has_text_matching expression="susceptibility"/>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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109 </assert_contents>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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110 </output>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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111 </test>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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112 <test>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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113 <param name="type" value="single"/>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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114 <param name="seq1" ftype="fastq.gz" value="reads.fastq.gz"/>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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115 <param name="species" value="sonnei"/>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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116 <param name="panel" value="20201012"/>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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117 <param name="format" value="json"/>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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118 <output name="output">
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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119 <assert_contents>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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120 <has_text_matching expression="susceptibility"/>
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121 </assert_contents>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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122 </output>
e8405163fb4e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
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123 </test>
0
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124 </tests>
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125 <help>
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126 @ATTRIBUTION@
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127 </help>
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128 <expand macro="citation" />
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129 </tool>