Mercurial > repos > iuc > hamronize_tool

annotate hamronize_tool.xml @ 4:cbfa52c8f1ef draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
author iuc
date Tue, 05 Mar 2024 19:47:12 +0000
parents e13b801516dd
children
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4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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1 <tool id="hamronize_tool" name="hAMRonize" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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2 <description>Antimicrobial Resistance Analysis Reports into a common data structure</description>
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3 <macros>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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4 <import>macros.xml</import>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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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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d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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7 <expand macro="requirements" />
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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8 <expand macro="version_command" />
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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9 <command detect_errors="exit_code"><![CDATA[
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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10 #import re
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11
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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12 #set $no_origin_info_tools = ['mykrobe', 'tbprofiler']
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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13 #set $origin_tools = ['abricate', 'amrfinderplus', 'fargene', 'srst2', 'staramr']
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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14 #set $in_fname_tools = ['amrfinderplus', 'amrplusplus', 'ariba', 'csstar', 'deeparg', 'fargene', 'groot', 'kmerresistance', 'pointfinder', 'resfarms', 'rgi', 'srax', 'srst2']
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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15 #set $ref_db_name_tools = ['ariba', 'csstar', 'groot', 'srax']
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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16 #set $input_file_name = re.sub('[^\s\w\-\.]', '_', str($input.report.element_identifier))
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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17
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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18 hamronize
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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19 '$input.tool'
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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20 '$input.report'
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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21 --format '$format'
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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22 --output '$output'
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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23 #if $input.tool not in $no_origin_info_tools
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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24 #if $input.tool in $origin_tools and $input.origin.origin
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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25 #if $input.origin.origin
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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26 --analysis_software_version '$input.report.tool_version'
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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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27 #else
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cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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28 --analysis_software_version '$input.origin.analysis_software_version'
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d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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29 #end if
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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30 --reference_database_version '$input.reference_database_version'
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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31 #else
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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32 --analysis_software_version '$input.analysis_software_version'
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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33 --reference_database_version '$input.reference_database_version'
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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34 #end if
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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35 #end if
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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36 #if $input.tool in $in_fname_tools
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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37 #if str($input.input_file_name) != ''
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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38 --input_file_name '$input.input_file_name'
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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39 #else
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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40 --input_file_name '$input_file_name'
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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41 #end if
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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42 #end if
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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43 #if $input.tool in $ref_db_name_tools
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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44 --reference_database_name '$input.reference_database_name'
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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45 #end if
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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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46 ]]> </command>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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47 <inputs>
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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48 <conditional name="input">
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49 <param name="tool" type="select" label="Tool">
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cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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50 <option value="abricate" selected="true">ABRicate</option>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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51 <option value="amrfinderplus">AMRFinderPlus</option>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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52 <option value="amrplusplus">AMRplusplus</option>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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53 <option value="ariba">ARIBA</option>
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54 <option value="csstar">c-SSTAR</option>
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55 <option value="deeparg">DeepARG</option>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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56 <option value="fargene">fARGene</option>
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57 <option value="groot">GROOT</option>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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58 <option value="kmerresistance">KmerResistance</option>
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59 <option value="mykrobe">Mykrobe</option>
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60 <option value="pointfinder">PointFinder</option>
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61 <option value="resfams">ResFams</option>
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62 <option value="resfinder">ResFinder</option>
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63 <option value="rgi">RGI</option>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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64 <option value="srax">SraX</option>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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65 <option value="srst2">SRST2</option>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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66 <option value="staramr">StarAMR</option>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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67 <option value="tbprofiler">TBProfiler</option>
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68 </param>
4
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69 <when value="abricate">
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70 <expand macro="report" format="tabular" label="ABRicate Report file"/>
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71 <expand macro="origin" software="ABRicate"/>
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72 </when>
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73 <when value="amrfinderplus">
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74 <expand macro="report" format="tabular" label="AMRFinderPlus Report file"/>
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75 <expand macro="input_file_name"/>
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76 <expand macro="origin" software="AMRFinderPlus"/>
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77 </when>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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78 <when value="amrplusplus">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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79 <expand macro="report" format="tabular" label="AMRplusplus gene report"/>
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80 <expand macro="input_file_name"/>
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81 <expand macro="analysis_software_version" software="AMRplusplus"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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82 <expand macro="reference_database_version"/>
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83 </when>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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84 <when value="ariba">
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85 <expand macro="report" format="tabular" label="ARIBA output"/>
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86 <expand macro="input_file_name"/>
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diff changeset
87 <expand macro="analysis_software_version" software="ARIBA"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
88 <expand macro="reference_database_version"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
89 <expand macro="reference_database_name" software="ARIBA"/>
0
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 <when value="csstar">
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
92 <expand macro="report" format="tabular" label="c-SSTAR output"/>
0
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"/>
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
94 <expand macro="analysis_software_version" software="c-SSTAR" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
95 <expand macro="reference_database_version"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
96 <expand macro="reference_database_name" software="c-SSTAR"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
97 </when>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
98 <when value="deeparg">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
99 <expand macro="report" format="tabular" label="DeepARG output"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
100 <expand macro="input_file_name"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
101 <expand macro="analysis_software_version" software="DeepARG"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
102 </when>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
103 <when value="fargene">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
104 <expand macro="report" format="txt" label="fARGene HMM Search Result"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
105 <expand macro="input_file_name"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
106 <expand macro="origin" software="fARGene"/>
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
107 </when>
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
108 <when value="groot">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
109 <expand macro="report" format="tabular" label="GROOT output"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
110 <expand macro="input_file_name"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
111 <expand macro="analysis_software_version" software="GROOT" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
112 <expand macro="reference_database_version"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
113 <expand macro="reference_database_name" software="GROOT"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
114 </when>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
115 <when value="kmerresistance">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
116 <expand macro="report" format="tabular" label="KmerResistance gene report"/>
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
117 <expand macro="input_file_name"/>
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
118 <expand macro="analysis_software_version" software="KmerResistance"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
119 <expand macro="reference_database_version"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
120 </when>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
121 <when value="mykrobe">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
122 <expand macro="report" format="json" label="Mykrobe Report file"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
123 </when>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
124 <when value="pointfinder">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
125 <param name="report" type="data" format="txt" label="PointFinder results"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
126 <expand macro="input_file_name"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
127 <expand macro="analysis_software_version" software="PointFinder"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
128 <expand macro="reference_database_version"/>
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
129 </when>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
130 <when value="resfams">
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
131 <param name="report" type="data" format="txt" label="ResFams results"/>
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
132 <expand macro="input_file_name"/>
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
133 <expand macro="analysis_software_version" software="ResFams"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
134 <expand macro="reference_database_version"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
135 </when>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
136 <when value="resfinder">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
137 <param name="report" type="data" format="tabular" label="ResFinder results"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
138 <expand macro="input_file_name"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
139 <expand macro="analysis_software_version" software="ResFinder"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
140 <expand macro="reference_database_version"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
141 </when>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
142 <when value="rgi">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
143 <param name="report" type="data" format="txt" label="RGI output"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
144 <expand macro="input_file_name"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
145 <expand macro="analysis_software_version" software="RGI"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
146 <expand macro="reference_database_version"/>
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
147 </when>
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
148 <when value="srax">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
149 <param name="report" type="data" format="tabular" label="SraX detected ARGs"/>
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
150 <expand macro="input_file_name"/>
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
151 <expand macro="analysis_software_version" software="SraX"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
152 <expand macro="reference_database_version"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
153 <expand macro="reference_database_name" software="SraX"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
154 </when>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
155 <when value="srst2">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
156 <expand macro="report" format="tabular" label="SRST2 report"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
157 <expand macro="input_file_name"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
158 <expand macro="origin" software="SRST2"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
159 </when>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
160 <when value="staramr">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
161 <expand macro="report" format="tabular" label="StarAMR ResFinder output"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
162 <expand macro="origin" software="StarAMR"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
163 </when>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
164 <when value="tbprofiler">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
165 <param name="report" type="data" format="tabular" label="TBProfiler output"/>
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
166 </when>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
167 </conditional>
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
168 <param argument="--format" type="select" label="Output format">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
169 <option value="tsv" selected="True">Tabular</option>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
170 <option value="json">JSON</option>
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
171 </param>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
172 </inputs>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
173 <outputs>
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
174 <data name="output" format="tabular" label="${tool.name} on ${on_string} (${input.tool})">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
175 <change_format>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
176 <when input="format" value="json" format="json"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
177 </change_format>
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
178 </data>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
179 </outputs>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
180 <tests>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
181 <!-- abricate -->
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
182 <test expect_num_outputs="1">
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
183 <conditional name="input">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
184 <param name="tool" value="abricate" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
185 <param name="report" value="abricate/report.tsv" ftype="tabular" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
186 <conditional name="origin">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
187 <param name="origin" value="false"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
188 <param name="analysis_software_version" value="tool_v_1"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
189 </conditional>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
190 <param name="reference_database_version" value="db_v_1"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
191 </conditional>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
192 <param name="format" value="tsv" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
193 <output name="output" ftype="tabular">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
194 <assert_contents>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
195 <has_n_lines n="8"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
196 <has_n_columns n="36"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
197 <has_text text="input_file_name"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
198 <has_text text="GCF_010120755.1_ASM1012075v1_genomic"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
199 <has_text text="vanS-M"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
200 <has_text text="db_v_1"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
201 </assert_contents>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
202 </output>
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
203 </test>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
204 <test expect_num_outputs="1">
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
205 <conditional name="input">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
206 <param name="tool" value="abricate" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
207 <param name="report" value="abricate/report.tsv" ftype="tabular" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
208 <conditional name="origin">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
209 <param name="origin" value="false"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
210 <param name="analysis_software_version" value="tool_v_1"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
211 </conditional>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
212 <param name="reference_database_version" value="db_v_1"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
213 </conditional>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
214 <param name="format" value="json" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
215 <output name="output" ftype="json">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
216 <assert_contents>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
217 <has_text text="input_file_name"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
218 <has_text text="GCF_010120755.1_ASM1012075v1_genomic"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
219 <has_text text="vanS-M"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
220 <has_text text="db_v_1"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
221 </assert_contents>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
222 </output>
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
223 </test>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
224 <!-- ariba -->
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
225 <test expect_num_outputs="1">
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
226 <conditional name="input">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
227 <param name="tool" value="ariba" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
228 <param name="report" value="ariba/report.tsv" ftype="tabular" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
229 <param name="input_file_name" value="ariba_report" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
230 <param name="analysis_software_version" value="ariba_v1" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
231 <param name="reference_database_version" value="db_v_1" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
232 <param name="reference_database_name" value="dbname" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
233 </conditional>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
234 <param name="format" value="tsv" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
235 <output name="output" ftype="tabular">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
236 <assert_contents>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
237 <has_n_lines n="257"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
238 <has_n_columns n="36"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
239 <has_text text="input_file_name"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
240 <has_text text="ariba_report"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
241 <has_text text="AAC_3__IId"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
242 <has_text text="ariba_v1"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
243 <has_text text="db_v_1"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
244 <has_text text="dbname"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
245 </assert_contents>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
246 </output>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
247 </test>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
248 <!-- mykrobe -->
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
249 <test expect_num_outputs="1">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
250 <conditional name="input">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
251 <param name="tool" value="mykrobe" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
252 <param name="report" value="mykrobe/mykrobe.json" ftype="json" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
253 </conditional>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
254 <param name="format" value="tsv" />
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
255 <output name="output" ftype="tabular">
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
256 <assert_contents>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
257 <has_n_lines n="2"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
258 <has_n_columns n="36"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
259 <has_text text="input_file_name"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
260 <has_text text="rpoB"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
261 <has_text text="v0.10.0"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
262 <has_text text="NC_000962.3"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
263 <has_text text="mykrobe"/>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
264 </assert_contents>
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
265 </output>
0
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
266 </test>
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
267 <!-- rgi -->
d2590ecc4189 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
iuc
parents:
diff changeset
268 <test expect_num_outputs="1">
4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents: 3
diff changeset
269 <conditional name="input">
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270 <param name="tool" value="rgi" />
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271 <param name="report" value="rgi/rgi.txt" ftype="txt" />
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272 <param name="analysis_software_version" value="rgi_v1" />
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273 <param name="reference_database_version" value="card_v1" />
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274 </conditional>
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275 <param name="format" value="tsv" />
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276 <output name="output" ftype="tabular">
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277 <assert_contents>
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278 <has_n_lines n="42"/>
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279 <has_n_columns n="36"/>
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280 <has_text text="input_file_name"/>
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281 <has_text text="rgi.txt"/>
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282 <has_text text="oqxA"/>
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283 <has_text text="CARD"/>
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284 <has_text text="card_v1"/>
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285 <has_text text="rgi_v1"/>
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286 </assert_contents>
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287 </output>
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288 </test>
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289 </tests>
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290 <help><![CDATA[
3
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291 **What it does**
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292
4
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293 hAMRonization parses multiple Antimicrobial Resistance Analysis Reports
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294 from disparate antimicrobial resistance gene detection tools into a single
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295 unified format.
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296
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297 This is an implementation of the hAMRonization AMR detection specification
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298 scheme which supports gene presence/absence resistance and mutational resistance
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299 (if supported by the underlying tool).
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300
3
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301 **Inputs**
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302
4
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303 Report or output of an antimicrobial resistance gene detection tool:
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304
3
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305 * abricate: abricate's output report i.e., OUTPUT.tsv
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306 * amrfinderplus: amrfinderplus's output report i.e., OUTPUT.tsv
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307 * ariba: ariba's output report i.e., OUTDIR/OUTPUT.tsv
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308 * rgi: rgi's output report i.e., OUTPUT.txt or OUTPUT_bwtoutput.gene_mapping_data.txt
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309 * resfinder: resfinder's output report i.e., data_resfinder.json
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310 * resfinder4: resfinder4's tabular output report i.e., ResFinder_results_tab.txt
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311 * srax: srax's output report i.e., sraX_detected_ARGs.tsv
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312 * deeparg: deeparg's output report i.e., OUTDIR/OUTPUT.mapping.ARG
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313 * kmerresistance: kmerresistance's output report i.e., OUTPUT.KmerRes
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314 * srst2: srst2's output report i.e., OUTPUT_srst2_report.tsv
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315 * staramr: staramr's output report i.e., resfinder.tsv
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316 * csstar: csstar's output report i.e., OUTPUT.tsv
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317 * amrplusplus: amrplusplus's output report i.e., gene.tsv
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318 * resfams: resfams's output report i.e., resfams.tblout
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319 * groot: groot's output report i.e., OUTPUT.tsv (from `groot report`)
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320
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321 More: https://github.com/pha4ge/hAMRonization/#usage
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322
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323 ]]></help>
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324 <expand macro="citations"/>
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325 </tool>