Mercurial > repos > tduigou > inchi_to_sink

annotate inchi_to_sink.xml @ 1:b560a9e57ccf draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Thu, 03 Feb 2022 14:18:42 +0000
parents ef125d2f57c3
children 3627d3e49889
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1 <tool id="inchi_to_sink" name="Inchi to sink" version="@TOOL_VERSION@" profile="19.09">
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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@">1.0.0</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="0.5">echo</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #set inchi=$source_inchi.rstrip()
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11 echo -e '"name","inchi"\n"$source_name","$inchi"' > '$sink'
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12 ]]></command>
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13 <inputs>
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14 <param name="source_inchi" type="text" label="Source InChI" optional="false">
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15 <validator type="empty_field" message="InChI string is required"/>
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16 </param>
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17 <param name="source_name" type="text" value="Biosensor" label="Source name">
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18 <validator type="empty_field" message="Source name is required"/>
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19 </param>
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20 </inputs>
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21 <outputs>
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22 <data name="sink" format="csv" label="${tool.name} - ${source_name}" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <!-- test 1: check if identical outputs are produced -->
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27 <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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28 <param name="source_name" value="Choline" />
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29 <output name="sink" file="sink_to-detect_choline.csv" ftype="csv" compare="diff"/>
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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33 Inchi to sink
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34 ===============
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35
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36 Convert Inchi string to CSV sink file for Retropath2.0 Input.
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37
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38 Input
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39 -----
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40
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41 Required:
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42
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43 * **source_inchi**\ : (string) Inchi string
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44
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45 Optional:
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46
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47 * **source_name**\ : (string) Inchi name (Default=target)
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48
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49
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50 Version
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51 ----------
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52
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53 1.0.0
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54
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55 Authors
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56 -------
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57
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58 * **Kenza BAZI KABBAJ**
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59
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60 ]]></help>
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61 </tool>