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comparison pangolin.xml @ 5:e2497d4385e2 draft default tip

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"planemo upload for repository https://github.com/hCoV-2019/pangolin commit 9e569ed56e07b5d2d3fb8a72ddc477d34570f081"
author nml
date Fri, 29 May 2020 00:37:50 -0400
parents 35566aadcfc7
children
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4:35566aadcfc7 5:e2497d4385e2
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' $additional.write_tree && 9 pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length' $additional.write_tree $additional.include_putative &&
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="include_putative" type="boolean" checked="false" argument="-p"
27 truevalue="-p"
28 falsevalue=""
29 label="Include putative lineages"
30 help="Putative lineages fit the criteria required for lineage designation but have not got recall values suitable for lineage assignment.
31 If left as 'No', only lineages with >95% recall rate will be used."
32 />
26 <param name="write_tree" type="boolean" checked="false" 33 <param name="write_tree" type="boolean" checked="false"
27 truevalue="--write-tree" 34 truevalue="--write-tree"
28 falsevalue="" 35 falsevalue=""
29 label="Write guide trees" 36 label="Write guide trees"
30 help="Output a collection of trees with each query sequence placed in the guide tree" 37 help="Output a collection of trees with each query sequence placed in the guide tree"
52 </test> 59 </test>
53 <test> 60 <test>
54 <param name="input1" value="test_seqs.fasta" /> 61 <param name="input1" value="test_seqs.fasta" />
55 <section name="additional"> 62 <section name="additional">
56 <param name="write_tree" value="true" /> 63 <param name="write_tree" value="true" />
64 <param name="include_putative" value="true" />
57 </section> 65 </section>
58 <output name="lineage_report" > 66 <output name="lineage_report" >
59 <assert_contents> 67 <assert_contents>
60 <has_text text="Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17" /> 68 <has_text text="Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17" />
61 <has_text text="USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16" /> 69 <has_text text="USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16" />