Mercurial > repos > iuc > data_manager_build_kma_index

comparison data_manager/kma_build_index.xml @ 0:889cc43b72d6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
author iuc
date Tue, 18 Feb 2020 16:24:23 -0500
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1 <?xml version="1.0"?>
2 <tool id="kma_build_index" name="KMA Index Builder" tool_type="manage_data" version="1.2.21+galaxy0" profile="19.01">
3 <description>kma index builder</description>
4 <requirements>
5 <requirement type="package" version="1.2.21">kma</requirement>
6 <requirement type="package" version="3.7">python</requirement>
7 </requirements>
8 <version_command>kma -v</version_command>
9 <command detect_errors="exit_code">
10 <![CDATA[
11 python '${__tool_directory__}/kma_build_index.py'
12 '${out_file}'
13 --k ${k}
14 --k_t ${k_t}
15 --k_i ${k_i}
16 --ML ${ML}
17 --ht ${ht}
18 --hq ${hq}
19 --name '${name}'
20 '${fasta}'
21 ]]>
22 </command>
23 <inputs>
24 <param name="k" type="integer" value="16" min="8" max="32" label="kmer size used for indexing the database." />
25 <param name="k_t" type="integer" value="16" min="8" max="32" label="kmer size used to identify template candidates when running KMA." />
26 <param name="k_i" type="integer" value="16" min="8" max="32" label="kmer size used when performing alignments between two sequences." />
27 <param name="ML" type="integer" value="16" label="Minimum length of templates" />
28 <param name="ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" />
29 <param name="hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" />
30 <param name="name" type="text" label="Name for index" />
31 <param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" />
32 </inputs>
33 <outputs>
34 <data name="out_file" format="data_manager_json" />
35 </outputs>
36 <tests>
37 <test>
38 <param name="fasta" value="phiX174.fasta"/>
39 <param name="name" value="index"/>
40 <output name="out_file" value="kma_data_manager.json" compare="sim_size" />
41 </test>
42 </tests>
43 <help>
44 </help>
45 <citations>
46 <citation type="doi">10.1186/s12859-018-2336-6</citation>
47 </citations>
48 </tool>