Mercurial > repos > matthias > data_manager_mitos

annotate data_manager/mitos_fetcher.xml @ 0:d1beb6fba192 draft default tip

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit a7354d02377105590891f7337f472dc2a2f224a4
author matthias
date Thu, 09 May 2019 16:20:33 -0400
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d1beb6fba192 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit a7354d02377105590891f7337f472dc2a2f224a4
matthias
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1 <?xml version="1.0"?>
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2 <tool id="mitos_fetcher_data_manager" name="MITOS" tool_type="manage_data" version="0.0.1">
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3 <description>reference data downloader</description>
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4 <command detect_errors="exit_code">
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5 <![CDATA[
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6 python '$__tool_directory__/data_manager.py'
d1beb6fba192 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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7 --out '${out_file}'
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8 --type '$type_cond.type_select'
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9 --db '$type_cond.database'
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10 ]]>
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11 </command>
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12 <inputs>
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13 <conditional name="type_cond">
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14 <param name="type_select" type="select" label="MITOS version">
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15 <option value="mitos">MITOS</option>
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16 <option value="mitos2">MITOS2</option>
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17 </param>
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18 <when value="mitos">
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19 <param name="database" type="select" label="Refernce data version">
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20 <option value="mitos1-refdata">RefSeq39 + MiTFi tRNA models</option>
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21 </param>
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22 </when>
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23 <when value="mitos2">
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24 <param name="database" type="select" label="Refernce data version">
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25 <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option>
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26 <option value="refseq63m">RefSeq63 Metazoa</option>
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27 <option value="refseq63f">RefSeq63 Fungi</option>
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28 <option value="refseq63o">RefSeq63 Opisthokonta</option>
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29 <option value="refseq81m">RefSeq81 Metazoa</option>
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30 <option value="refseq81f">RefSeq81 Fungi</option>
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31 <option value="refseq81o">RefSeq81 Opisthokonta</option>
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32 </param>
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33 </when>
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34 </conditional>
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35 </inputs>
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36 <outputs>
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37 <data name="out_file" format="data_manager_json" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 <conditional name="type_cond">
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42 <param name="type_select" value="mitos"/>
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43 <param name="database" value="mitos1-refdata"/>
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44 </conditional>
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45 <output name="out_file" file="mitos_refseq39.json"/>
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46 </test>
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47 </tests>
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48 <help>
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49 TODO
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50 </help>
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51 </tool>
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52