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comparison pangolin.xml @ 2:c897e502c084 draft

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"planemo upload for repository https://github.com/hCoV-2019/pangolin commit b53db6d0612f94e5c9365c9ecd267eeff396097f"
author nml
date Mon, 04 May 2020 16:40:54 -0400
parents b91b3923656e
children 24c005390360
comparison
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1:b91b3923656e 2:c897e502c084
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 8
9 pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length' && 9 pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length' $additional.write_tree &&
10 10
11 sed 's/,/\t/g' lineage_report.csv > lineage_report.tsv 11 sed 's/,/\t/g' lineage_report.csv > lineage_report.tsv
12 ]]></command> 12 ]]></command>
13 <inputs> 13 <inputs>
14 <param name="input1" type="data" format="fasta" 14 <param name="input1" type="data" format="fasta"
21 /> 21 />
22 <param name="min_length" type="integer" value="10000" min="0" 22 <param name="min_length" type="integer" value="10000" min="0"
23 label="Minimum query length to attempt assignment" 23 label="Minimum query length to attempt assignment"
24 argument="--min-length" 24 argument="--min-length"
25 /> 25 />
26 <param name="write_tree" type="boolean" checked="false"
27 truevalue="--write-tree"
28 falsevalue=""
29 label="Write guide trees"
30 help="Output a collection of trees with each query sequence placed in the guide tree"
31 />
26 </section> 32 </section>
27 </inputs> 33 </inputs>
28 <outputs> 34 <outputs>
29 <data format="tabular" from_work_dir="lineage_report.tsv" name="lineage_report" label="${input1.name}_lineage_report" /> 35 <data format="tabular" from_work_dir="lineage_report.tsv" name="lineage_report" label="${input1.name}_lineage_report" />
36 <collection name="pangolin_trees" type="list" label="${tool.name} Trees">
37 <filter>additional['write_tree']</filter>
38 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tree" directory="pangolin_trees/" format="iqtree" />
39 </collection>
30 </outputs> 40 </outputs>
31 <tests> 41 <tests>
32 <test> 42 <test>
33 <param name="input1" value="test_seqs.fasta" /> 43 <param name="input1" value="test_seqs.fasta" />
34 <output name="lineage_report" value="lineage_report.tsv" /> 44 <output name="lineage_report" value="lineage_report.tsv" />
45 </test>
46 <test>
47 <param name="input1" value="test_seqs.fasta" />
48 <section name="additional">
49 <param name="write_tree" value="true" />
50 </section>
51 <output name="lineage_report" value="lineage_report.tsv" />
52 <output_collection name="pangolin_trees" type="list">
53 <element name="USA_NY-NYUMC7_2020_EPI_ISL_418192__USA_New_York_Manhattan_2020-03-16" ftype="iqtree">
54 <assert_contents>
55 <has_text text="USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16" />
56 </assert_contents>
57 </element>
58 <element name="Japan_DP0779_2020_EPI_ISL_416626__Japan_unknown__2020-02-17" ftype="iqtree">
59 <assert_contents>
60 <has_text text="Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17" />
61 </assert_contents>
62 </element>
63 </output_collection>
35 </test> 64 </test>
36 </tests> 65 </tests>
37 <help><![CDATA[ 66 <help><![CDATA[
38 67
39 Pangolin 68 Pangolin