Mercurial > repos > iuc > hamronize_summarize

comparison hamronize_summarize.xml @ 1:a84e3131ae6a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b872ea086ebd98be64839e7bbb1ddf7a181943d0"
author iuc
date Sat, 23 Oct 2021 21:37:48 +0000
parents ef76d74a7171
children 6e2731b13533
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0:ef76d74a7171 1:a84e3131ae6a
1 <tool id="hamronize_summarize" name="summarize" version="@VERSION@+galaxy0"> 1 <tool id="hamronize_summarize" name="summarize" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description> harmorization reports</description> 2 <description> harmorization reports</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6
7 <expand macro="requirements" /> 6 <expand macro="requirements" />
8 <expand macro="version_command" /> 7 <expand macro="version_command" />
9
10 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
11 #for $counter, $report in enumerate($reports): 9 #for $counter, $report in enumerate($reports):
12 #if $report.is_of_type('tsv', 'tabular'): 10 #if $report.is_of_type('tsv', 'tabular'):
13 #set $ext = 'tsv' 11 #set $ext = 'tsv'
14 #elif $report.is_of_type('json'): 12 #elif $report.is_of_type('json'):
29 *.tsv 27 *.tsv
30 *.json 28 *.json
31 ]]> </command> 29 ]]> </command>
32 30
33 <inputs> 31 <inputs>
34 <param name="reports" type="data" multiple="true" format="tsv,json" label="Report files"/> 32 <param name="reports" type="data" multiple="true" format="tabular,json" label="Report files"/>
35 <param name="summary_type" type="select" label="Output format" multiple="false"> 33 <param name="summary_type" type="select" label="Output format" multiple="false">
36 <option value="tsv">tsv</option> 34 <option value="tsv">tsv</option>
37 <option value="json">json</option> 35 <option value="json">json</option>
38 <option value="interactive">interactive</option> 36 <option value="interactive">interactive</option>
39 </param> 37 </param>
40 </inputs> 38 </inputs>
41 39
42 <outputs> 40 <outputs>
43 <data format="tsv" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="output.tsv"> 41 <data format="tabular" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="output.tsv">
44 <filter>summary_type == "tsv"</filter> 42 <filter>summary_type == "tsv"</filter>
45 </data> 43 </data>
46 <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="output.json"> 44 <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="output.json">
47 <filter>summary_type == "json"</filter> 45 <filter>summary_type == "json"</filter>
48 </data> 46 </data>
53 <tests> 51 <tests>
54 <!-- tsv output --> 52 <!-- tsv output -->
55 <test expect_num_outputs="1"> 53 <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" /> 54 <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" /> 55 <param name="summary_type" value="tsv" />
58 <output name="output_tsv" ftype="tsv" file="summary.tsv" /> 56 <output name="output_tsv" ftype="tabular" file="summary.tsv" />
59 </test> 57 </test>
60 <!-- json output --> 58 <!-- json output -->
61 <test expect_num_outputs="1"> 59 <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" /> 60 <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" /> 61 <param name="summary_type" value="json" />