Mercurial > repos > thanhlv > hamronization

comparison hamronize_summarize.xml @ 0:5fca34360c12 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
author thanhlv
date Tue, 02 Feb 2021 21:18:52 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:5fca34360c12
1 <tool id="hamronize_summarize" name="hamronize_summarize" version="@VERSION@+galaxy0">
2 <description> harmorize 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 ]]>
76 </help>
77 </tool>