Mercurial > repos > iuc > hamronize_tool

annotate hamronize_tool.xml @ 1:ec82fac4eb4b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0"
author iuc
date Sat, 23 Oct 2021 21:38:09 +0000
parents d2590ecc4189
children e13b801516dd
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ec82fac4eb4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0"
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1 <tool id="hamronize_tool" name="hamronize" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
0
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2 <description> parse multiple Antimicrobial Resistance Analysis Reports into a common data structure</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8
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9 <command detect_errors="exit_code"><![CDATA[
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10 #set $extra_2_params = str("ariba,srax,csstar,groot").split(",")
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11 #set $extra_1_param = $extra_2_params + str("amrfinderplus,rgi,resfinder4,deeparg,kmerresistance,srst2,amrplusplus,resfarms").split(",")
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12
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13 hamronize
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14 ${select_tool.tool}
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15 --analysis_software_version '${analysis_software_version}'
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16 --reference_database_version '${reference_database_version}'
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17 --format ${output_format}
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18 #if $output_format == "tsv"
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19 --output hamronized.tsv
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20 #else
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21 --output hamronized.json
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22 #end if
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23
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24 #if $select_tool.tool in $extra_1_param
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25 --input_file_name $select_tool.input_file_name
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26 #end if
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27
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28 #if $select_tool.tool in $extra_2_params
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29 --reference_database_id $select_tool.reference_database_id
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30 #end if
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31
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32 $report
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33 ]]> </command>
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34
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35 <inputs>
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36 <param name="report" type="data" format="txt,tabular" label="Report file"/>
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37 <conditional name="select_tool">
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38 <param name="tool" type="select" label="Tool">
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39 <option value="abricate" selected="true">abricate</option>
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40 <option value="amrfinderplus">amrfinderplus</option>
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41 <option value="ariba">ariba</option>
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42 <option value="rgi">rgi</option>
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43 <option value="resfinder">resfinder</option>
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44 <option value="resfinder4">resfinder4</option>
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45 <option value="srax">srax</option>
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46 <option value="deeparg">deeparg</option>
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47 <option value="kmerresistance">kmerresistance</option>
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48 <option value="srst2">srst2</option>
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49 <option value="staramr">staramr</option>
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50 <option value="csstar">csstar</option>
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51 <option value="amrplusplus">amrplusplus</option>
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52 <option value="resfams">resfams</option>
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53 <option value="groot">groot</option>
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54 </param>
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55 <when value="abricate" />
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56 <when value="resfinder" />
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57 <when value="staramr" />
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58 <when value="amrfinderplus">
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59 <expand macro="input_file_name"/>
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60 </when>
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61
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62 <when value="ariba">
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63 <expand macro="input_file_name"/>
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64 <expand macro="reference_database_id"/>
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65 </when>
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66
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67 <when value="rgi">
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68 <expand macro="input_file_name"/>
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69 </when>
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70
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71 <when value="resfinder4">
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72 <expand macro="input_file_name"/>
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73 </when>
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74
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75 <when value="srax">
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76 <expand macro="input_file_name"/>
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77 <expand macro="reference_database_id"/>
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78 </when>
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79
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80 <when value="deeparg">
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81 <expand macro="input_file_name"/>
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82 </when>
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83
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84 <when value="kmerresistance">
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85 <expand macro="input_file_name"/>
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86 </when>
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87
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88 <when value="srst2">
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89 <expand macro="input_file_name"/>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
90 </when>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
91
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
92 <when value="csstar">
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
93 <expand macro="input_file_name"/>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
94 <expand macro="reference_database_id"/>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
95 </when>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
96
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
97 <when value="amrplusplus">
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
98 <expand macro="input_file_name"/>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
99 </when>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
100
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
101 <when value="resfams">
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
102 <expand macro="input_file_name"/>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
103 </when>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
104
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
105 <when value="groot">
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
106 <expand macro="input_file_name"/>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
107 <expand macro="reference_database_id"/>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
108 </when>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
109 </conditional>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
110 <param name="output_format" type="select" label="Output format" multiple="false" display="radio">
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
111 <option value="tsv" selected="True">tsv</option>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
112 <option value="json">json</option>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
113 </param>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
114 <param name="analysis_software_version" type="text" label="Analysis software version"></param>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
115 <param name="reference_database_version" type="text" label="Reference database version"></param>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
116 </inputs>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
117
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
118 <outputs>
1
ec82fac4eb4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0"
iuc
parents: 0
diff changeset
119 <data format="tabular" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.tsv">
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
120 <filter>output_format == "tsv"</filter>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
121 </data>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
122 <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.json">
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
123 <filter>output_format == "json"</filter>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
124 </data>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
125 </outputs>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
126 <tests>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
127 <!-- abricate -->
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
128 <test expect_num_outputs="1">
1
ec82fac4eb4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0"
iuc
parents: 0
diff changeset
129 <param name="report" value="abricate/report.tsv" ftype="tabular" />
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
130 <param name="tool" value="abricate" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
131 <param name="output_format" value="tsv" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
132 <param name="reference_database_version" value="db_v_1" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
133 <param name="analysis_software_version" value="tool_v_1" />
1
ec82fac4eb4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0"
iuc
parents: 0
diff changeset
134 <output name="output_tsv" file="hamronized_abricate.tsv" ftype="tabular" />
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
135 </test>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
136 <test expect_num_outputs="1">
1
ec82fac4eb4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0"
iuc
parents: 0
diff changeset
137 <param name="report" value="abricate/report.tsv" ftype="tabular" />
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
138 <param name="tool" value="abricate" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
139 <param name="output_format" value="json" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
140 <param name="reference_database_version" value="db_v_1" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
141 <param name="analysis_software_version" value="tool_v_1" />
1
ec82fac4eb4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0"
iuc
parents: 0
diff changeset
142 <output name="output_json" file="hamronized_abricate.json" ftype="json" />
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
143 </test>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
144 <!-- ariba -->
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
145 <test expect_num_outputs="1">
1
ec82fac4eb4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0"
iuc
parents: 0
diff changeset
146 <param name="report" value="ariba/report.tsv" ftype="tabular" />
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
147 <param name="tool" value="ariba" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
148 <param name="output_format" value="tsv" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
149 <param name="reference_database_version" value="db_v_1" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
150 <param name="analysis_software_version" value="ariba_v1" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
151 <param name="input_file_name" value="ariba_report" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
152 <param name="reference_database_id" value="dbname" />
1
ec82fac4eb4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0"
iuc
parents: 0
diff changeset
153 <output name="output_tsv" file="hamronized_ariba.tsv" ftype="tabular" />
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
154 </test>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
155 <!-- rgi -->
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
156 <test expect_num_outputs="1">
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
157 <param name="report" value="rgi/rgi.txt" ftype="txt" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
158 <param name="tool" value="rgi" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
159 <param name="output_format" value="tsv" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
160 <param name="reference_database_version" value="card_v1" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
161 <param name="analysis_software_version" value="rgi_v1" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
162 <param name="input_file_name" value="rgi_report" />
1
ec82fac4eb4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0"
iuc
parents: 0
diff changeset
163 <output name="output_tsv" file="hamronized_rgi.tsv" ftype="tabular"/>
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
164 </test>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
165 </tests>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
166 <help><![CDATA[
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
167 **What it does**
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
168 Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
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diff changeset
169
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
170 **Inputs**
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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diff changeset
171
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
172 ::
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
173
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
174 Tools with hAMRonizable reports:
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
175 {abricate,amrfinderplus,ariba,rgi,resfinder,resfinder4,srax,deeparg,kmerresistance,srst2,staramr,csstar,amrplusplus,resfams,groot}
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
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176 abricate hAMRonize abricate's output report i.e., OUTPUT.tsv
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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177 amrfinderplus hAMRonize amrfinderplus's output report i.e., OUTPUT.tsv
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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178 ariba hAMRonize ariba's output report i.e., OUTDIR/OUTPUT.tsv
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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179 rgi hAMRonize rgi's output report i.e., OUTPUT.txt or OUTPUT_bwtoutput.gene_mapping_data.txt
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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180 resfinder hAMRonize resfinder's output report i.e., data_resfinder.json
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181 resfinder4 hAMRonize resfinder4's tabular output report i.e., ResFinder_results_tab.txt
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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182 srax hAMRonize srax's output report i.e., sraX_detected_ARGs.tsv
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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183 deeparg hAMRonize deeparg's output report i.e., OUTDIR/OUTPUT.mapping.ARG
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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184 kmerresistance hAMRonize kmerresistance's output report i.e., OUTPUT.KmerRes
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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185 srst2 hAMRonize srst2's output report i.e., OUTPUT_srst2_report.tsv
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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186 staramr hAMRonize staramr's output report i.e., resfinder.tsv
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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187 csstar hAMRonize csstar's output report i.e., OUTPUT.tsv
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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188 amrplusplus hAMRonize amrplusplus's output report i.e., gene.tsv
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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189 resfams hAMRonize resfams's output report i.e., resfams.tblout
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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190 groot hAMRonize groot's output report i.e., OUTPUT.tsv (from `groot report`)
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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191
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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192
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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193
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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194 ::
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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195
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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196 More: https://github.com/pha4ge/hAMRonization/#usage
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197
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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198 ]]> </help>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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199 </tool>