Mercurial > repos > tduigou > rptools_rpcompletion

annotate rpcompletion.xml @ 1:c33bde07cbc7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit c1b249f25f3143e21980cd7daecb1aebb88ef948-dirty
author tduigou
date Fri, 24 Oct 2025 08:37:01 +0000
parents 874093da8436
children
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1 <tool id="rptools_rpcompletion" name="Complete Reactions"
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2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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3 <description>Completes mono-component reactions output by RetroPath2.0 with the appropriate
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4 cofactors</description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <stdio>
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10 <exit_code range="1" level="fatal" description="Could not Xref compartment_id" />
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11 <exit_code range="2" level="fatal" description="ValueError returned" />
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12 <regex match="Continuing without sink molecule" source="both" level="warning"
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13 description="The sink file is empty or not found" />
0
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14 </stdio>
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15 <command detect_errors="exit_code"><![CDATA[
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16 TMPDIR="\${TMPDIR:-.}/rr_cache" &&
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17 mkdir -p "\${TMPDIR}" &&
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18 #if str($sink.cond) == 'empty'
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19 echo '"Name","InChI"' > empty_sink.csv &&
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20 #set sinkfile='empty_sink.csv'
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21 #else
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22 #set sinkfile=$sink.sinkfile
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23 #end if
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24
0
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25 python -m rptools.rpcompletion
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26 '$rp2_pathways'
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27 $sinkfile
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28 '$rp2paths_compounds'
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29 '$rp2paths_pathways'
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30 completed_pathways
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31 --upper_flux_bound '$adv.upper_flux_bound'
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32 --lower_flux_bound '$adv.lower_flux_bound'
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33 --max_subpaths_filter '$adv.max_subpaths_filter'
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34 --chemical-space '$adv.chemical_space'
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35 #if $adv.cofile
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36 --cofactors '$adv.cofile'
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37 #end if
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38 #if not $sink.error_codes
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39 --silent
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40 #end if
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41 --cache-dir "\${TMPDIR:-.}"
0
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42 ]]></command>
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43 <inputs>
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44 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
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45 <param name="rp2paths_compounds" type="data" format="tabular" label="RP2paths compounds" />
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46 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
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47 <conditional name="sink">
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48 <param name="cond" type="select" label="Empty sink">
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49 <option value="provided" selected="True">Provided</option>
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50 <option value="empty">Empty</option>
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51 </param>
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52 <when value="provided">
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53 <param name="sinkfile" type="data" format="csv" label="Sink File"
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54 help="Sink file which comprises all compounds that are considered as granted in your system." />
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55 <param name="error_codes" type="boolean" checked="true"
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56 label="Return error codes" />
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57 </when>
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58 <when value="empty">
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59 <param name="error_codes" type="boolean" checked="false"
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60 label="Return error codes" />
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61 </when>
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62 </conditional>
0
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63 <section name="adv" title="Advanced Options" expanded="false">
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64 <param argument="max_subpaths_filter" type="integer" value="10" min="0"
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65 label="Max subpaths generated per pathway"
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66 help="Maximal number of subpaths to be created per master pathway." />
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67 <param argument="upper_flux_bound" type="integer" value="10000" min="-10000" max="10000"
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68 label="Upper flux bound"
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69 help="Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
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70 <param argument="lower_flux_bound" type="integer" value="-10000" min="-10000"
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71 max="10000" label="Lower flux bound"
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72 help="Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
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73 <param name="chemical_space" type="select" label="Chemical space">
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74 <option value="mnx4.4" selected="True">mnx4.4</option>
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75 <option value="mnx3.1">mnx3.1</option>
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76 </param>
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77 <param name="cofile" type="data" format="txt,tsv,tabular" optional="True"
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78 label="Cofactor file" />
0
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79 </section>
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80 </inputs>
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81 <outputs>
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82 <collection name="pathways" type="list" label="${tool.name}">
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83 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml" format="xml"
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84 directory="completed_pathways" visible="false" />
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85 </collection>
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86 </outputs>
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87 <tests>
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88 <test>
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89 <!-- test 1: check if outputs are represented in an expected number -->
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90 <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" />
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91 <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
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92 <param name="rp2_pathways" value="1-rp2_metnet.csv" />
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93 <conditional name="sink">
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94 <param name="cond" value="provided" />
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95 <param name="sinkfile" value="2-sink.csv" />
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96 </conditional>
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97 <output_collection name="pathways" type="list" count="10" />
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98 </test>
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99 </tests>
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100 <help><![CDATA[
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101 rpCompletion
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102 ============
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103
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104 Completes mono-component reactions output by `RetroPath2.0 <https://www.doi.org/10.1016/j.ymben.2017.12.002>`_ 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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105
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106 Output
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107 ------
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108
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109 * **pathways**: SBML completed pathways
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110 ]]></help>
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111 <expand macro="creator" />
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112 <citations>
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113 <citation type="doi">10.1038/s41467-022-32661-x</citation>
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114 </citations>
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115 </tool>