Mercurial > repos > iuc > hamronize_summarize

comparison hamronize_summarize.xml @ 0:ef76d74a7171 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
author iuc
date Tue, 16 Mar 2021 12:39:05 +0000
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children a84e3131ae6a
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-1:000000000000 0:ef76d74a7171
1 <tool id="hamronize_summarize" name="summarize" version="@VERSION@+galaxy0">
2 <description> harmorization reports</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="requirements" />
8 <expand macro="version_command" />
9
10 <command detect_errors="exit_code"><![CDATA[
11 #for $counter, $report in enumerate($reports):
12 #if $report.is_of_type('tsv', 'tabular'):
13 #set $ext = 'tsv'
14 #elif $report.is_of_type('json'):
15 #set $ext = 'json'
16 #end if
17 ln -s '$report' ./report_${counter}.${ext} &&
18 #end for
19
20 hamronize summarize
21 --summary_type $summary_type
22 #if $summary_type == "tsv"
23 --output output.tsv
24 #elif $summary_type == "json"
25 --output output.json
26 #else
27 --output output.html
28 #end if
29 *.tsv
30 *.json
31 ]]> </command>
32
33 <inputs>
34 <param name="reports" type="data" multiple="true" format="tsv,json" label="Report files"/>
35 <param name="summary_type" type="select" label="Output format" multiple="false">
36 <option value="tsv">tsv</option>
37 <option value="json">json</option>
38 <option value="interactive">interactive</option>
39 </param>
40 </inputs>
41
42 <outputs>
43 <data format="tsv" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="output.tsv">
44 <filter>summary_type == "tsv"</filter>
45 </data>
46 <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="output.json">
47 <filter>summary_type == "json"</filter>
48 </data>
49 <data format="html" name="output_html" label="${tool.name} on ${on_string}: Output" from_work_dir="output.html">
50 <filter>summary_type == "interactive"</filter>
51 </data>
52 </outputs>
53 <tests>
54 <!-- tsv output -->
55 <test expect_num_outputs="1">
56 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
57 <param name="summary_type" value="tsv" />
58 <output name="output_tsv" ftype="tsv" file="summary.tsv" />
59 </test>
60 <!-- json output -->
61 <test expect_num_outputs="1">
62 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
63 <param name="summary_type" value="json" />
64 <output name="output_json" ftype="json">
65 <assert_contents>
66 <has_text text="GCF_010120755.1_ASM1012075v1_genomic" />
67 <has_text text="H_NS.3000676.BA000007.3.1737690_1738104.5476" />
68 <has_text text="NODE_9_length_203843_cov_42.4911_20" />
69 </assert_contents>
70 </output>
71 </test>
72 </tests>
73 <help>
74 <![CDATA[
75 **What it does**
76 This tool will take a list of report and create single sorted report in the specified format just containing the unique entries across input reports. It can handle mixed json and tsv hamronized report formats
77
78 **Inputs**
79 A list of hamronize reports
80 ]]>
81 </help>
82 </tool>