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comparison tn93_filter.xml @ 0:ba95715078c9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
author iuc
date Fri, 23 Apr 2021 03:05:08 +0000
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1 <tool id="tn93_filter" name="TN93 Filter" version="@VERSION@">
2 <description>- remove sequences from a reference that are within a given distance of of a cluster</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@VERSION@">tn93</requirement>
8 <requirement type="package" version="1.70">biopython</requirement>
9 </requirements>
10 <version_command><![CDATA[tn93 --version]]></version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 cat '$reads' > filtered_msa.fa &&
13 tn93 -o pairwise.csv -s filtered_msa.fa -t $threshold '$clusters' &&
14 python '$__tool_directory__/tn93_filter.py' --reference '$reference'
15 --distances pairwise.csv
16 --reads filtered_msa.fa
17 --clusters '$clusters'
18 ]]></command>
19 <inputs>
20 <param name="reads" type="data" format="fasta" label="Aligned reads" />
21 <param name="reference" type="data" format="fasta" label="Reference sequence" />
22 <param name="clusters" type="data" format="fasta" label="FASTA file with compressed clusters" />
23 <param name="threshold" type="float" value="0.015" label="Pairwise distance threshold" />
24 </inputs>
25 <outputs>
26 <data name="filtered_reference" format="fasta" from_work_dir="filtered_msa.fa" />
27 </outputs>
28 <tests>
29 <test>
30 <param name="reads" value="filter-in1-reads.fa" />
31 <param name="reference" value="filter-in1-reference.fa" />
32 <param name="clusters" value="filter-in1-clusters.fa" />
33 <param name="threshold" value="0.35" />
34 <output name="filtered_reference" file="filter-out1.fasta" ftype="fasta" />
35 </test>
36 </tests>
37 <help><![CDATA[
38 TN93-Filter
39 ===========
40
41 Removes aligned sequences that are within a given distance from a reference
42 sequence using the 1993 Tamura-Nei distance calculation.
43 ]]></help>
44 <expand macro="citations">
45 <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation>
46 </expand>
47 </tool>