Mercurial > repos > iuc > hamronize_summarize

comparison 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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4:f8bcc852f6b3 5:88045b4d5597
1 <tool id="hamronize_summarize" name="hamronize: summarize" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> 1 <tool id="hamronize_summarize" name="hamronize summarize:" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description> harmorization reports</description> 2 <description>Concatenate and summarize AMR detection reports</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 #for $counter, $report in enumerate($reports): 10 #for $counter, $report in enumerate($reports):
11 #if $report.is_of_type('tsv', 'tabular'): 11 #if $report.is_of_type('tsv', 'tabular'):
12 #set $ext = 'tsv' 12 #set $ext = 'tsv'
13 #elif $report.is_of_type('json'): 13 #elif $report.is_of_type('json'):
14 #set $ext = 'json' 14 #set $ext = 'json'
15 #end if 15 #end if
16 ln -s '$report' ./report_${counter}.${ext} && 16 ln -s '$report' 'report_${counter}.${ext}' &&
17 #end for 17 #end for
18 18
19 hamronize summarize 19 hamronize
20 --summary_type $summary_type 20 summarize
21 #if $summary_type == "tsv" 21 --summary_type '$summary_type'
22 --output output.tsv 22 --output '$output'
23 #elif $summary_type == "json" 23 report_*
24 --output output.json 24 ]]></command>
25 #else
26 --output output.html
27 #end if
28 ./report_*
29 ]]> </command>
30
31 <inputs> 25 <inputs>
32 <param name="reports" type="data" multiple="true" format="tabular,json" label="Report files"/> 26 <param name="reports" type="data" multiple="true" format="tabular,json" label="Report files"/>
33 <param name="summary_type" type="select" label="Output format" multiple="false"> 27 <param argument="--summary_type" type="select" label="Output format" multiple="false">
34 <option value="tsv">tsv</option> 28 <option value="tsv">Tabular</option>
35 <option value="json">json</option> 29 <option value="json">JSON</option>
36 <option value="interactive">interactive</option> 30 <option value="interactive">Interactive HTML</option>
37 </param> 31 </param>
38 </inputs> 32 </inputs>
39
40 <outputs> 33 <outputs>
41 <data format="tabular" name="output_tsv" label="${tool.name} on ${on_string}: Table" from_work_dir="output.tsv"> 34 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Concatenated and summarized reports" from_work_dir="output.tsv">
42 <filter>summary_type == "tsv"</filter> 35 <change_format>
43 </data> 36 <when input="summary_type" value="json" format="json"/>
44 <data format="json" name="output_json" label="${tool.name} on ${on_string}: JSON" from_work_dir="output.json"> 37 <when input="summary_type" value="interactive" format="html"/>
45 <filter>summary_type == "json"</filter> 38 </change_format>
46 </data>
47 <data format="html" name="output_html" label="${tool.name} on ${on_string}: Interactive" from_work_dir="output.html">
48 <filter>summary_type == "interactive"</filter>
49 </data> 39 </data>
50 </outputs> 40 </outputs>
51 <tests> 41 <tests>
52 <!-- tsv output --> 42 <!-- tsv output -->
53 <test expect_num_outputs="1"> 43 <test expect_num_outputs="1">
54 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" /> 44 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
55 <param name="summary_type" value="tsv" /> 45 <param name="summary_type" value="tsv" />
56 <output name="output_tsv" ftype="tabular" file="summary.tsv" /> 46 <output name="output" ftype="tabular">
47 <assert_contents>
48 <has_n_lines n="155"/>
49 <has_n_columns n="37"/>
50 <has_text text="GCF_010120755.1_ASM1012075v1_genomic" />
51 <has_text text="ariba_report" />
52 <has_text text="rgi_report" />
53 </assert_contents>
54 </output>
57 </test> 55 </test>
58 <!-- json output --> 56 <!-- json output -->
59 <test expect_num_outputs="1"> 57 <test expect_num_outputs="1">
60 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" /> 58 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
61 <param name="summary_type" value="json" /> 59 <param name="summary_type" value="json" />
62 <output name="output_json" ftype="json"> 60 <output name="output" ftype="json">
63 <assert_contents> 61 <assert_contents>
64 <has_text text="GCF_010120755.1_ASM1012075v1_genomic" /> 62 <has_text text="GCF_010120755.1_ASM1012075v1_genomic" />
65 <has_text text="H_NS.3000676.BA000007.3.1737690_1738104.5476" /> 63 <has_text text="ariba_report" />
66 <has_text text="NODE_9_length_203843_cov_42.4911_20" /> 64 <has_text text="rgi_report" />
65 </assert_contents>
66 </output>
67 </test>
68 <!-- html output -->
69 <test expect_num_outputs="1">
70 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
71 <param name="summary_type" value="interactive" />
72 <output name="output" ftype="html">
73 <assert_contents>
74 <has_text text="GCF_010120755.1_ASM1012075v1_genomic" />
75 <has_text text="ariba_report" />
76 <has_text text="rgi_report" />
67 </assert_contents> 77 </assert_contents>
68 </output> 78 </output>
69 </test> 79 </test>
70 </tests> 80 </tests>
71 <help> 81 <help><![CDATA[
72 <![CDATA[ 82 **What it does**
73 **What it does** 83
74 This tool will take a list of report and create single sorted report in the specified format 84 This tool will take a list of report and create single sorted report in the specified format
75 just containing the unique entries across input reports. It can handle mixed json and tsv hamronized report formats 85 just containing the unique entries across input reports. It can handle mixed json and tsv hamronized report formats
76 **Inputs** 86
77 A list of hamronize reports 87 **Inputs**
78 88 A list of hamronize reports
79 ]]> 89 ]]></help>
80 </help>
81 <expand macro="citations"/> 90 <expand macro="citations"/>
82 </tool> 91 </tool>