Mercurial > repos > bgruening > get_pubchem

annotate get_pubchem_as_smiles.xml @ 1:4d966d5bdd17 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:27:00 -0400
parents cd19c3fab3a6
children
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4d966d5bdd17 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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1 <tool id="ctb_pubchem_download_as_smiles" name="PubChem Download" version="0.3" >
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cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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2 <description>as canonical SMILES</description>
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3 <requirements>
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4d966d5bdd17 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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4 <requirement type="package" version="3.1.1">openbabel</requirement>
4d966d5bdd17 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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5 <requirement type="package" version="3">python</requirement>
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6 </requirements>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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7 <stdio>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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8 <regex match="obError"
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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9 source="both"
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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10 level="fatal"
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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11 description="Critical Open Babel error" />
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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12 <regex match="obWarning"
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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13 source="both"
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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14 level="warning"
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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15 description="Non-critical Open Babel warning" />
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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16 <regex match="obInfo"
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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17 source="both"
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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18 level="log"
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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19 description="Open Babel Information" />
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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20 </stdio>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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21 <command>
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22 <![CDATA[
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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23 python '$__tool_directory__/get_pubchem_as_smiles.py'
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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24 -o $pubchem_smi
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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25 -p \${GALAXY_SLOTS:-4}
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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26 ## temporary hack until my Galaxy patch is committed
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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27 > /dev/null 2>&1
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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28 ]]>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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29 </command>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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30 <inputs>
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31 </inputs>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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32 <outputs>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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33 <data format="smi" name="pubchem_smi" />
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34 </outputs>
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35 <tests>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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36 </tests>
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37 <help>
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38 <![CDATA[
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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39
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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40 .. class:: infomark
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41
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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42 **What this tool does**
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43
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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44 This tool will fetch one PubChem_ file after another and convert them to canonical SMILES.
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45
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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46 .. _PubChem: http://pubchem.ncbi.nlm.nih.gov/
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47
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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48 -----
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49
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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50 .. class:: infomark
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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51
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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52 **Output**
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53
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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54 The output will be one large SMILES file.
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55
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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56 ]]>
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57 </help>
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58 </tool>