Mercurial > repos > iuc > hamronize_tool

annotate hamronize_tool.xml @ 3:e13b801516dd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
author iuc
date Fri, 09 Feb 2024 21:27:18 +0000
parents ec82fac4eb4b
children cbfa52c8f1ef
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1 <tool id="hamronize_tool" name="hamronize" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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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>
3
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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10 <command detect_errors="exit_code"><![CDATA[
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11 #set $extra_2_params = str("ariba,srax,csstar,groot").split(",")
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12 #set $extra_1_param = $extra_2_params + str("amrfinderplus,rgi,resfinder4,deeparg,kmerresistance,srst2,amrplusplus,resfarms").split(",")
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14 hamronize
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15 ${select_tool.tool}
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16 --analysis_software_version '${analysis_software_version}'
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17 --reference_database_version '${reference_database_version}'
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18 --format ${output_format}
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19 #if $output_format == "tsv"
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20 --output hamronized.tsv
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21 #else
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22 --output hamronized.json
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23 #end if
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24
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25 #if $select_tool.tool in $extra_1_param
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26 --input_file_name $select_tool.input_file_name
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27 #end if
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28
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29 #if $select_tool.tool in $extra_2_params
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30 --reference_database_id $select_tool.reference_database_id
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31 #end if
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32
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33 $report
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34 ]]> </command>
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35
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36 <inputs>
1
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37 <param name="report" type="data" format="txt,tabular" label="Report file"/>
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38 <conditional name="select_tool">
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39 <param name="tool" type="select" label="Tool">
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40 <option value="abricate" selected="true">abricate</option>
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41 <option value="amrfinderplus">amrfinderplus</option>
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42 <option value="ariba">ariba</option>
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43 <option value="rgi">rgi</option>
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44 <option value="resfinder">resfinder</option>
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45 <option value="resfinder4">resfinder4</option>
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46 <option value="srax">srax</option>
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47 <option value="deeparg">deeparg</option>
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48 <option value="kmerresistance">kmerresistance</option>
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49 <option value="srst2">srst2</option>
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50 <option value="staramr">staramr</option>
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51 <option value="csstar">csstar</option>
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52 <option value="amrplusplus">amrplusplus</option>
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53 <option value="resfams">resfams</option>
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54 <option value="groot">groot</option>
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55 </param>
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56 <when value="abricate" />
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57 <when value="resfinder" />
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58 <when value="staramr" />
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59 <when value="amrfinderplus">
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60 <expand macro="input_file_name"/>
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61 </when>
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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 <when value="rgi">
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67 <expand macro="input_file_name"/>
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68 </when>
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69 <when value="resfinder4">
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70 <expand macro="input_file_name"/>
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71 </when>
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72 <when value="srax">
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73 <expand macro="input_file_name"/>
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74 <expand macro="reference_database_id"/>
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75 </when>
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76 <when value="deeparg">
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77 <expand macro="input_file_name"/>
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78 </when>
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79 <when value="kmerresistance">
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80 <expand macro="input_file_name"/>
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81 </when>
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82 <when value="srst2">
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83 <expand macro="input_file_name"/>
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84 </when>
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85 <when value="csstar">
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86 <expand macro="input_file_name"/>
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87 <expand macro="reference_database_id"/>
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88 </when>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
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89 <when value="amrplusplus">
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
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90 <expand macro="input_file_name"/>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
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91 </when>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
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92 <when value="resfams">
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
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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:
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94 </when>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
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95 <when value="groot">
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
96 <expand macro="input_file_name"/>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
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97 <expand macro="reference_database_id"/>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
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98 </when>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
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99 </conditional>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
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100 <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"
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101 <option value="tsv" selected="True">tsv</option>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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102 <option value="json">json</option>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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103 </param>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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104 <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:
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105 <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"
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106 </inputs>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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107
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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108 <outputs>
3
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parents: 1
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109 <data format="tabular" name="output_tsv" label="${tool.name} on ${on_string}: Table" from_work_dir="hamronized.tsv">
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
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110 <filter>output_format == "tsv"</filter>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
111 </data>
3
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
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parents: 1
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112 <data format="json" name="output_json" label="${tool.name} on ${on_string}: JSON" from_work_dir="hamronized.json">
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
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113 <filter>output_format == "json"</filter>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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114 </data>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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115 </outputs>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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116 <tests>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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117 <!-- abricate -->
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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118 <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
119 <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
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120 <param name="tool" value="abricate" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
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121 <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
122 <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
123 <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
124 <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
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125 </test>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
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126 <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
127 <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"
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128 <param name="tool" value="abricate" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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129 <param name="output_format" value="json" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
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130 <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
131 <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"
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parents: 0
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132 <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"
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133 </test>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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134 <!-- ariba -->
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
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135 <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
136 <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"
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137 <param name="tool" value="ariba" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
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138 <param name="output_format" value="tsv" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
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139 <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
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140 <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
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141 <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
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142 <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
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143 <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"
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144 </test>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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145 <!-- rgi -->
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
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146 <test expect_num_outputs="1">
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
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147 <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"
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148 <param name="tool" value="rgi" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
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149 <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:
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150 <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
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151 <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
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152 <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"
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parents: 0
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153 <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"
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154 </test>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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155 </tests>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
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156 <help><![CDATA[
3
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
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157 **What it does**
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158
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
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159 Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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160
3
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
iuc
parents: 1
diff changeset
161 **Inputs**
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162
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
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163 Depends on the tools with hAMRonizable reports:
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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164
3
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
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165 * abricate: abricate's output report i.e., OUTPUT.tsv
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iuc
parents: 1
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166 * amrfinderplus: amrfinderplus's output report i.e., OUTPUT.tsv
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
iuc
parents: 1
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167 * ariba: ariba's output report i.e., OUTDIR/OUTPUT.tsv
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
iuc
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168 * rgi: rgi's output report i.e., OUTPUT.txt or OUTPUT_bwtoutput.gene_mapping_data.txt
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
iuc
parents: 1
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169 * resfinder: resfinder's output report i.e., data_resfinder.json
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
iuc
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170 * resfinder4: resfinder4's tabular output report i.e., ResFinder_results_tab.txt
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
iuc
parents: 1
diff changeset
171 * srax: srax's output report i.e., sraX_detected_ARGs.tsv
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
iuc
parents: 1
diff changeset
172 * deeparg: deeparg's output report i.e., OUTDIR/OUTPUT.mapping.ARG
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
iuc
parents: 1
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173 * kmerresistance: kmerresistance's output report i.e., OUTPUT.KmerRes
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
iuc
parents: 1
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174 * srst2: srst2's output report i.e., OUTPUT_srst2_report.tsv
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
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175 * staramr: staramr's output report i.e., resfinder.tsv
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
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176 * csstar: csstar's output report i.e., OUTPUT.tsv
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
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177 * amrplusplus: amrplusplus's output report i.e., gene.tsv
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
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178 * resfams: resfams's output report i.e., resfams.tblout
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
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179 * groot: groot's output report i.e., OUTPUT.tsv (from `groot report`)
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d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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180
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181 More: https://github.com/pha4ge/hAMRonization/#usage
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182
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183 ]]></help>
e13b801516dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
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184 <expand macro="citations"/>
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d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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185 </tool>