Mercurial > repos > thanhlv > hamronization

annotate 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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
1 <tool id="hamronize_summarize" name="hamronize_summarize" version="@VERSION@+galaxy0">
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
2 <description> harmorize reports</description>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
3 <macros>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
4 <import>macros.xml</import>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
5 </macros>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
6
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
7 <expand macro="requirements" />
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
8 <expand macro="version_command" />
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
9
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
11 #for $counter, $report in enumerate($reports):
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
12 #if $report.is_of_type('tsv', 'tabular'):
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
13 #set $ext = 'tsv'
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
14 #elif $report.is_of_type('json'):
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
15 #set $ext = 'json'
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
16 #end if
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
17 ln -s '$report' ./report_${counter}.${ext} &&
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
18 #end for
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
19
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
20 hamronize summarize
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
21 --summary_type $summary_type
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
22 #if $summary_type == "tsv"
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
23 --output output.tsv
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
24 #elif $summary_type == "json"
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
25 --output output.json
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
26 #else
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
27 --output output.html
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
28 #end if
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
29 *.tsv
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
30 *.json
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
31 ]]> </command>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
32
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
33 <inputs>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
34 <param name="reports" type="data" multiple="true" format="tsv,json" label="Report files"/>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
35 <param name="summary_type" type="select" label="Output format" multiple="false">
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
36 <option value="tsv">tsv</option>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
37 <option value="json">json</option>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
38 <option value="interactive">interactive</option>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
39 </param>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
40 </inputs>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
41
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
42 <outputs>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
43 <data format="tsv" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="output.tsv">
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
44 <filter>summary_type == "tsv"</filter>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
45 </data>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
46 <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="output.json">
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
47 <filter>summary_type == "json"</filter>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
48 </data>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
49 <data format="html" name="output_html" label="${tool.name} on ${on_string}: Output" from_work_dir="output.html">
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
50 <filter>summary_type == "interactive"</filter>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
51 </data>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
52 </outputs>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
53 <tests>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
54 <!-- tsv output -->
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
55 <test expect_num_outputs="1">
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
56 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
57 <param name="summary_type" value="tsv" />
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
58 <output name="output_tsv" ftype="tsv" file="summary.tsv" />
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
59 </test>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
60 <!-- json output -->
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
61 <test expect_num_outputs="1">
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
62 <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
63 <param name="summary_type" value="json" />
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
64 <output name="output_json" ftype="json">
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
65 <assert_contents>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
66 <has_text text="GCF_010120755.1_ASM1012075v1_genomic" />
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
67 <has_text text="H_NS.3000676.BA000007.3.1737690_1738104.5476" />
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
68 <has_text text="NODE_9_length_203843_cov_42.4911_20" />
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
69 </assert_contents>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
70 </output>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
71 </test>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
72 </tests>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
73 <help>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
74 <![CDATA[
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
75 ]]>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
76 </help>
5fca34360c12 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/hamronization commit f4357e288c6ab3d1abf0dd8a8b4ccee72cbf1924-dirty"
thanhlv
parents:
diff changeset
77 </tool>