Mercurial > repos > iuc > data_manager_mitos

comparison data_manager/data_manager_mitos.xml @ 2:19d9be08560c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
author iuc
date Sun, 22 Nov 2020 18:03:14 +0000
parents 26a6f95e82c8
children d9339bb8127e
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1:1ff9996995ee 2:19d9be08560c
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.1"> 2 <tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.2">
3 <description>reference data downloader</description> 3 <description>reference data downloader</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.7">python</requirement> 5 <requirement type="package" version="3.7">python</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
23 <option value="mitos1-refdata">RefSeq39 + MiTFi tRNA models</option> 23 <option value="mitos1-refdata">RefSeq39 + MiTFi tRNA models</option>
24 </param> 24 </param>
25 </when> 25 </when>
26 <when value="mitos2"> 26 <when value="mitos2">
27 <param name="database" type="select" label="Reference data version"> 27 <param name="database" type="select" label="Reference data version">
28 <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option>
29 <option value="refseq63m">RefSeq63 Metazoa</option> 28 <option value="refseq63m">RefSeq63 Metazoa</option>
30 <option value="refseq63f">RefSeq63 Fungi</option> 29 <option value="refseq63f">RefSeq63 Fungi</option>
31 <option value="refseq63o">RefSeq63 Opisthokonta</option> 30 <option value="refseq63o">RefSeq63 Opisthokonta</option>
32 <option value="refseq89m">RefSeq89 Metazoa</option> 31 <option value="refseq89m">RefSeq89 Metazoa</option>
33 <option value="refseq89f">RefSeq89 Fungi</option> 32 <option value="refseq89f">RefSeq89 Fungi</option>
34 <option value="refseq89o">RefSeq89 Opisthokonta</option> 33 <option value="refseq89o">RefSeq89 Opisthokonta</option>
34 <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option>
35 </param> 35 </param>
36 </when> 36 </when>
37 </conditional> 37 </conditional>
38 </inputs> 38 </inputs>
39 <outputs> 39 <outputs>
44 <conditional name="type_cond"> 44 <conditional name="type_cond">
45 <param name="type_select" value="mitos"/> 45 <param name="type_select" value="mitos"/>
46 <param name="database" value="mitos1-refdata"/> 46 <param name="database" value="mitos1-refdata"/>
47 </conditional> 47 </conditional>
48 <output name="out_file" file="mitos_refseq39.json"/> 48 <output name="out_file" file="mitos_refseq39.json"/>
49 </test>
50 <test>
51 <conditional name="type_cond">
52 <param name="type_select" value="mitos2"/>
53 <param name="database" value="refseq63m"/>
54 </conditional>
55 <output name="out_file" file="mitos2_refseq63.json"/>
49 </test> 56 </test>
50 </tests> 57 </tests>
51 <help> 58 <help>
52 This data manager downloads MITOS and MITOS2 reference data for use in Galaxy. 59 This data manager downloads MITOS and MITOS2 reference data for use in Galaxy.
53 60
72 79
73 - protein data bases derived from the corresponding RefSeq release Donath et al. 2019 80 - protein data bases derived from the corresponding RefSeq release Donath et al. 2019
74 - covariance models computed for the data in the RefSeq releas based on the MITOS1 models 81 - covariance models computed for the data in the RefSeq releas based on the MITOS1 models
75 - in addition for Metazoa Release 63 also hidden markov models are available as described in Al Arab et al. 2017 82 - in addition for Metazoa Release 63 also hidden markov models are available as described in Al Arab et al. 2017
76 83
77 Data is downloaded from https://zenodo.org/record/3685310. 84 Data is downloaded from https://zenodo.org/record/4284483.
78 </help> 85 </help>
79 <citations> 86 <citations>
80 <citation type="doi">10.1016/j.ympev.2012.08.023</citation> 87 <citation type="doi">10.1016/j.ympev.2012.08.023</citation>
81 <citation type="doi">10.1093/nar/gkr1131</citation> 88 <citation type="doi">10.1093/nar/gkr1131</citation>
82 <citation type="doi">10.1016/j.ympev.2016.09.024</citation> 89 <citation type="doi">10.1016/j.ympev.2016.09.024</citation>