Mercurial > repos > tduigou > inchi_to_sink

annotate inchi_to_sink.xml @ 3:47f49582d8db draft

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
author tduigou
date Mon, 01 May 2023 01:27:27 +0000
parents 3627d3e49889
children
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47f49582d8db planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
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1 <tool id="inchi_to_sink" name="Inchi to sink" version="@TOOL_VERSION@" profile="19.09" license="MIT">
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2 <description>Convert InChI input to CSV sink</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.0.1</token>
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5 </macros>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #set inchi=$source_inchi.rstrip()
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8 echo -e '"name","inchi"\n"$source_name","$inchi"' > '$sink'
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9 ]]></command>
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10 <inputs>
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11 <param name="source_inchi" type="text" label="Source InChI" optional="false">
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12 <validator type="empty_field" message="InChI string is required"/>
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13 </param>
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14 <param name="source_name" type="text" value="Biosensor" label="Source name">
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15 <validator type="empty_field" message="Source name is required"/>
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16 </param>
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17 </inputs>
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18 <outputs>
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19 <data name="sink" format="csv" label="${tool.name} - ${source_name}" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <!-- test 1: check if identical outputs are produced -->
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24 <param name="source_inchi" value="InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1" />
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25 <param name="source_name" value="Choline" />
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26 <output name="sink" file="sink_to-detect_choline.csv" ftype="csv" compare="diff"/>
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30 Inchi to sink
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31 ===============
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32
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33 Convert Inchi string to CSV sink file for Retropath2.0 Input.
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34
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35 Input
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36 -----
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37
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38 Required:
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39
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40 * **source_inchi**\ : (string) Inchi string
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41
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42 Optional:
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43
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44 * **source_name**\ : (string) Inchi name (Default=Biosensor)
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45 ]]></help>
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46 <creator>
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47 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
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48 </creator>
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49 <citations>
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50 <citation type="bibtex">
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51 @unpublished{inchi_to_sink
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52 title = {{inchi_to_sink}},
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53 url = {https://github.com/brsynth/},
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54 }
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55 </citation>
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56 </citations>
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57 </tool>