Mercurial > repos > tduigou > rptools_rpcompletion

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 162ee89a8e36033f32973d72dfc1b11ca27da61f
author tduigou
date Fri, 01 Dec 2023 14:29:29 +0000
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1 <tool id="rptools_rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <stdio>
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8 <exit_code range="1" level="fatal" description="Could not Xref compartment_id" />
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9 <exit_code range="2" level="fatal" description="ValueError returned" />
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10 </stdio>
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11 <command detect_errors="exit_code"><![CDATA[
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12 python -m rptools.rpcompletion
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13 '$rp2_pathways'
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14 '$sink'
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15 '$rp2paths_compounds'
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16 '$rp2paths_pathways'
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17 completed_pathways
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18 --upper_flux_bound '$adv.upper_flux_bound'
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19 --lower_flux_bound '$adv.lower_flux_bound'
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20 --max_subpaths_filter '$adv.max_subpaths_filter'
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21 --cache-dir "\${TMPDIR:-.}"
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22 ]]></command>
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23 <inputs>
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24 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
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25 <param name="rp2paths_compounds" type="data" format="csv" label="RP2paths compounds" />
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26 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
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27 <param name="sink" type="data" format="csv" label="Sink from SBML" />
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28 <section name="adv" title="Advanced Options" expanded="false">
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29 <param argument="max_subpaths_filter" type="integer" value="10" min="1" max="1000" label="Max subpaths generated per pathway" help="Maximal number of subpaths to be created per master pathway." />
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30 <param argument="upper_flux_bound" type="integer" value="10000" min="-10000" max="10000" label="Upper flux bound" help="Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
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31 <param argument="lower_flux_bound" type="integer" value="-10000" min="-10000" max="10000" label="Lower flux bound" help="Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
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32 </section>
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33 </inputs>
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34 <outputs>
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35 <collection name="pathways" type="list" label="${tool.name}">
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36 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml" format="xml" directory="completed_pathways" visible="false" />
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37 </collection>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <!-- test 1: check if outputs are represented in an expected number -->
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42 <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" />
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43 <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
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44 <param name="rp2_pathways" value="1-rp2_metnet.csv" />
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45 <param name="sink" value="2-sink.csv" />
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46 <output_collection name="pathways" type="list" count="9"/>
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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50 rpCompletion
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51 ============
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52
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53 Completes mono-component reactions output by `RetroPath2.0 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data.
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54
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55 Input
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56 -----
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57
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58 Required:
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59
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60 * **RetroPath2.0 metabolic network**: RetroPath2.0 pathways file
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61 * **Sink from SBML**: rpextractsink file containing infos on molecules in the sink
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62 * **RP2paths compounds**: rp2paths compounds file
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63 * **RP2paths pathways**: rp2paths pathways file
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64
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65 Advanced options:
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66
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67 * **Upper flux bound**: (integer, default=9999) Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created.
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68 * **Lower flux bound**: (integer, default=0) Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created.
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69 * **Max subpaths generated per pathway**: (integer, default=10, 0=nofilter) Maximal number of subpaths to be created per master pathway.
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70
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71 Output
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72 ------
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73
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74 * **pathways**: SBML completed pathways
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75 ]]></help>
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76 <expand macro="creator"/>
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77 <citations>
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78 <citation type="doi">10.1038/s41467-022-32661-x</citation>
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79 </citations>
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80 </tool>