Mercurial > repos > matthias > data_manager_megan_tools

annotate data_manager/megan_tools_fetcher.xml @ 6:2aadd067ea24 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_megan_tools commit 00e65802fca3de53129deae7b6df0fd0111400d8-dirty
author matthias
date Mon, 05 Nov 2018 03:30:04 -0500
parents ba3aab283a68
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
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1 <?xml version="1.0"?>
5
ba3aab283a68 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit c529846e9c5cf125d11dd8d4f843cfadf7da3cec-dirty
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2 <tool id="megan_tools_fetcher" name="megan tools" tool_type="manage_data" version="0.0.3">
0
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
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3 <description>Mapping files downloader</description>
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4 <command detect_errors="exit_code">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
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5 <![CDATA[
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
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6 python '$__tool_directory__/data_manager.py'
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
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7 --out '${out_file}'
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
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8 --file '$type_cond.database_name'
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9 ]]>
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10 </command>
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11 <inputs>
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12 <conditional name="type_cond">
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13 <param name="type_select" type="select" label="mapping type">
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14 <option value="ncbi_current">Mapping files for current NCBI-nr protein database (not containing GI numbers)</option>
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15 <option value="silva">Mapping file for working with the SILVA SSU database</option>
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16 <option value="ncbi_deprecated">Deprecated mapping files for NCBI-nr protein database (releases until August 2016, containing GI numbers):</option>
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17 </param>
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18 <when value="ncbi_current">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
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19 <param name="database_name" type="select" label="mapping data">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
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20 <option value="prot_acc2tax-June2018X1.abin.zip">Protein accession to NCBI-taxonomy (June2018X1)</option>
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21 <option value="nucl_acc2tax-June2018.abin.zip">Nucleotide accession to NCBI-taxonomy (June2018)</option>
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22 <option value="acc2interpro-June2018X.abin.zip">Protein accession to InterPro (June2018X)</option>
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23 <option value="acc2eggnog-Oct2016X.abin.zip">Protein accession to eggNOG (Oct2016X)</option>
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24 <option value="acc2seed-May2015XX.abin.zip">Protein accession to SEED (May2015XX)</option>
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25 <option value="acc2kegg-Dec2017X1-ue.abin.zip">Protein accession to KEGG (Dec2017X1). Only for use with the Ultimate Edition of MEGAN.</option>
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26 </param>
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27 </when>
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28 <when value="silva">
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29 <param name="database_name" type="select" label="mapping data">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
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30 <option value="SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz">SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
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31 <option value="SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz">SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
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32 </param>
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33 </when>
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34 <when value="ncbi_deprecated">
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35 <param name="database_name" type="select" label="mapping data">
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36 <option value="prot_gi2tax-Aug2016X.bin.zip">Protein accession to NCBI-taxonomy (Aug2016X)</option>
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37 <option value="nucl_gi2tax-Aug2016.bin.zip">Nucleotide accession to NCBI-taxonomy (Aug2016)</option>
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38 <option value="gi2eggnog-June2016X.bin.zip">Protein accession to InterPro (June2016X)</option>
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39 <option value="gi2interpro-June2016X.bin.zip">Protein accession to eggNOG (June2016X)</option>
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40 <option value="gi2seed-May2015X.bin.zip">Protein accession to SEED (May2015X)</option>
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41 <option value="gi2kegg-Aug2016X-ue.bin.zip">Protein accession to KEGG (Aug2016X). Only for use with the Ultimate Edition of MEGAN.</option>
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42 </param>
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43 </when>
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44 </conditional>
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45 </inputs>
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46 <outputs>
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47 <data name="out_file" format="data_manager_json" />
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48 </outputs>
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49 <tests>
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50 <test>
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51 <conditional name="type_cond">
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52 <param name="type_select" value="silva"/>
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53 <param name="database_name" value="SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz"/>
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54 </conditional>
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55 <output name="out_file" file="SSURef_Nr99_132_tax_silva_to_NCBI_synonyms_json"/>
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56 </test>
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57 </tests>
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58 <help>
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59 TODO
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60 </help>
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61 </tool>
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62