Mercurial > repos > bgruening > get_online_data

annotate get_online_data.xml @ 0:deb08c131d50 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
author bgruening
date Wed, 22 May 2019 07:42:51 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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1 <tool id="ctb_online_data_fetch" name="Online data" version="0.4">
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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2 <description>fetching</description>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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3 <requirements>
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4 <requirement type="package" version="3">python</requirement>
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5 </requirements>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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6 <command>
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7 <![CDATA[
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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8 python '$__tool_directory__/get_online_data.py'
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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9 --url '$url_paste'
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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10 --out '$output'
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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11 --whitelist '$whitelist'
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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12 ]]>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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13 </command>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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14 <inputs>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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15 <param name="url_paste" type="text" area="true" size="5x55" label="URLs" help="List of URLs (one per line)."/>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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16 <param name="whitelist" type="text" area="true" size="10x20"
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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17 label="Whitelist of filename extensions"
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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18 help="Specify a list of file extensions which should be extracted (default: sdf, mol, smi, inchi). Each extension should be placed on a new line."/>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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19 </inputs>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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20 <outputs>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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21 <data format="txt" name="output" />
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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22 </outputs>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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23 <tests>
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24 <test>
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25 <param name="url_paste" value="https://github.com/simonbray/test-files/blob/master/get_online_data/1AKI.pdb.gz?raw=true" />
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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26 <param name="whitelist" value=".pdb"/>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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27 <output name="output" file="gztest.txt" />
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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28 </test>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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29 <test>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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30 <param name="url_paste" value="https://github.com/simonbray/test-files/blob/master/get_online_data/sdfs.zip?raw=true" />
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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31 <output name="output" file="ziptest.txt" />
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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32 </test>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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33 </tests>
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34 <help>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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35 <![CDATA[
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36
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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37 .. class:: infomark
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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38
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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39 **What this tool does**
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40
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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41 Fetch data via FTP or HTTP and store them in your history. Supply one or more URLs; all files with the chosen file extensions will be extracted. Caution: all files are concatenated together.
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42
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43 -----
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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44
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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45 .. class:: infomark
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46
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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47 **Input**
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48
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49 Supported filetypes are:
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50 - gz/gzip
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51 - ZIP (with recursive extracting of specific filetypes)
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52
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53
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54 ]]>
deb08c131d50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_online_data commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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55 </help>
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56 <citations>
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57 </citations>
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58 </tool>