Mercurial > repos > iuc > hamronize_summarize

annotate hamronize_summarize.xml @ 5:88045b4d5597 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 19:47:21 +0000
parents f8bcc852f6b3
children
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5
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1 <tool id="hamronize_summarize" name="hamronize summarize:" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>Concatenate and summarize AMR detection reports</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
4
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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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9 <command detect_errors="exit_code"><![CDATA[
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10 #for $counter, $report in enumerate($reports):
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11 #if $report.is_of_type('tsv', 'tabular'):
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12 #set $ext = 'tsv'
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13 #elif $report.is_of_type('json'):
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14 #set $ext = 'json'
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15 #end if
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16 ln -s '$report' 'report_${counter}.${ext}' &&
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17 #end for
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18
5
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19 hamronize
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20 summarize
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21 --summary_type '$summary_type'
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22 --output '$output'
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23 report_*
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24 ]]></command>
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25 <inputs>
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26 <param name="reports" type="data" multiple="true" format="tabular,json" label="Report files"/>
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27 <param argument="--summary_type" type="select" label="Output format" multiple="false">
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28 <option value="tsv">Tabular</option>
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29 <option value="json">JSON</option>
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30 <option value="interactive">Interactive HTML</option>
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31 </param>
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32 </inputs>
ef76d74a7171 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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33 <outputs>
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34 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Concatenated and summarized reports" from_work_dir="output.tsv">
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35 <change_format>
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36 <when input="summary_type" value="json" format="json"/>
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37 <when input="summary_type" value="interactive" format="html"/>
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38 </change_format>
0
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39 </data>
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40 </outputs>
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41 <tests>
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42 <!-- tsv output -->
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43 <test expect_num_outputs="1">
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44 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
ef76d74a7171 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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45 <param name="summary_type" value="tsv" />
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46 <output name="output" ftype="tabular">
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47 <assert_contents>
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48 <has_n_lines n="155"/>
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49 <has_n_columns n="37"/>
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50 <has_text text="GCF_010120755.1_ASM1012075v1_genomic" />
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51 <has_text text="ariba_report" />
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52 <has_text text="rgi_report" />
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53 </assert_contents>
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54 </output>
0
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55 </test>
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56 <!-- json output -->
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57 <test expect_num_outputs="1">
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58 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
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59 <param name="summary_type" value="json" />
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60 <output name="output" ftype="json">
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61 <assert_contents>
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62 <has_text text="GCF_010120755.1_ASM1012075v1_genomic" />
5
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63 <has_text text="ariba_report" />
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64 <has_text text="rgi_report" />
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65 </assert_contents>
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66 </output>
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67 </test>
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68 <!-- html output -->
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69 <test expect_num_outputs="1">
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70 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
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71 <param name="summary_type" value="interactive" />
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72 <output name="output" ftype="html">
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73 <assert_contents>
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74 <has_text text="GCF_010120755.1_ASM1012075v1_genomic" />
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75 <has_text text="ariba_report" />
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76 <has_text text="rgi_report" />
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77 </assert_contents>
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78 </output>
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79 </test>
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80 </tests>
5
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81 <help><![CDATA[
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82 **What it does**
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83
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84 This tool will take a list of report and create single sorted report in the specified format
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85 just containing the unique entries across input reports. It can handle mixed json and tsv hamronized report formats
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86
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87 **Inputs**
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88 A list of hamronize reports
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89 ]]></help>
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f8bcc852f6b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d
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90 <expand macro="citations"/>
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ef76d74a7171 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
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91 </tool>