Mercurial > repos > iuc > hamronize_summarize
comparison hamronize_summarize.xml @ 0:ef76d74a7171 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit 17562209ea2b5b8b28f229a5c305e468b04be58e"
author | iuc |
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date | Tue, 16 Mar 2021 12:39:05 +0000 |
parents | |
children | a84e3131ae6a |
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-1:000000000000 | 0:ef76d74a7171 |
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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> |