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Commit message:
planemo upload for repository https://github.com/brsynth/rp2paths commit 1a817217fcd199ae61266ec6133137a87f4ab4be-dirty |
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modified:
rp2paths.xml |
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| diff -r 016ae4a7705e -r 4462f4c997ba rp2paths.xml --- a/rp2paths.xml Wed Jul 24 08:42:00 2024 +0000 +++ b/rp2paths.xml Fri Oct 03 12:18:46 2025 +0000 |
| [ |
| b'@@ -1,14 +1,14 @@\n <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT">\n <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>\n <macros>\n- <token name="@TOOL_VERSION@">1.5.1</token>\n+ <token name="@TOOL_VERSION@">2.1.0</token>\n </macros>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>\n </requirements>\n <stdio>\n <regex match="TIMEOUT:" level="fatal" />\n- <regex match="ERROR:" level="fatal" />\n+ <regex match="ERROR:" level="fatal" />\n <regex match="WARNING:" level="warning" />\n </stdio>\n <command detect_errors="exit_code"><![CDATA[\n@@ -16,7 +16,44 @@\n python -m rp2paths all\n \'$rp2_pathways\'\n --outdir out\n- --timeout \'$adv.timeout\' &&\n+ --timeout \'$adv.timeout\' \n+ #if str($adv.forward) == \'true\'\n+ --forward\n+ #end if\n+ #if $adv.cofile\n+ --cofile \'$adv.cofile\'\n+ #end if\n+ #if str($adv.mindepth) == \'true\'\n+ --minDepth\n+ #end if\n+ #if $adv.sink\n+ --customsinkfile \'$adv.sink\'\n+ #end if\n+ --maxsteps \'$adv.maxsteps\'\n+ --maxpaths \'$adv.maxpaths\'\n+ #if str($adv.unfold) == \'true\'\n+ --unfold_compounds\n+ #end if\n+ #set cmp_ids = []\n+ #for $x in $adv.rep_include_path\n+ #silent cmp_ids.append(str($x.cmp_id))\n+ #end for\n+ #if len(cmp_ids) > 0\n+ #set cmp_id = \' \'.join($cmp_ids)\n+ --onlyPathsStartingBy $cmp_id\n+ #end if\n+ #set cmp_ids = []\n+ #for $x in $adv.rep_exclude_path\n+ #silent cmp_ids.append(str($x.cmp_id))\n+ #end for\n+ #if len(cmp_ids) > 0\n+ #set cmp_id = \' \'.join($cmp_ids)\n+ --notPathsStartingBy $cmp_id\n+ #end if \n+ #if $adv.cmpfile\n+ --cmpdnamefile \'$adv.cmpfile\'\n+ #end if\n+ --target \'$adv.target\' &&\n mv out/compounds.txt out/compounds.tsv &&\n cp out/compounds.tsv \'$compounds\' &&\n if test -f \'out/out_paths.csv\'; then\n@@ -24,21 +61,63 @@\n fi\n ]]></command>\n <inputs>\n- <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis."/>\n+ <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways"\n+ help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis." />\n <section name="adv" title="Advanced Options" expanded="false">\n- <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." />\n+ <param name="timeout" type="integer" value="1800" label="Time Out"\n+ help="Time out before killing a process (in seconds), default: 30 minutes." />\n+ <param\n+ name="forward" type="boolean" checked="false" label="Forward"\n+ help="Consider reactions in the forward direction" />\n+ <param name="cofile"\n+ type="data" format="csv" optional="True" label="List of cofactors" />\n+ <param\n+ name="mindepth" type="boolean" checked="false" label="Minimal depth scope"\n+ help="Use minimal depth scope, i.e. stop the scope computation as as soon an a first minimal path linking target to sink is found" />\n+ <param\n+ name="sink" type="data" format="tabular" optional="True" label="List of sinks"\n+ help="Listing compounds to consider as sink compounds. Sink compounds should be provided by their IDs, as used in the reaction.erx'..b'="20" label="Max pathways"\n+ help="Cutoff on the maximum number of pathways. 0 (default) for unlimited number of pathways" />\n+ <param\n+ name="unfold" type="boolean" checked="false" label="Unfold pathways"\n+ help="Unfold pathways based on equivalencie of compounds (can lead to combinatorial explosion)." />\n+ <repeat name="rep_include_path" title="Include path starting by">\n+ <param name="cmp_id" type="text" label="Path label"\n+ help="List of compounds IDs to consider. If specified, only paths making use of at least one of these compounds as initial substrate (first step of a pathway) are kept.">\n+ <validator type="empty_field" message="Not empty" />\n+ </param>\n+ </repeat>\n+ <repeat name="rep_exclude_path" title="Include path starting by">\n+ <param name="cmp_id" type="text" label="Path label"\n+ help="List of compounds IDs. If specifed, paths making use of one of these compounds as unique initial substrate will be filtered out">\n+ <validator type="empty_field" message="Not empty" />\n+ </param>\n+ </repeat>\n+ <param name="cmpfile" type="data" format="tabular"\n+ optional="True" label="List of compounds" help="File with name of compounds" />\n+ <param\n+ name="target" type="text" value="TARGET_0000000001"\n+ label="Target compound internal ID"\n+ help="This internal ID specifies which compound should be considered as the targeted compound. The default behavior is to consider as the target the first compound used as a source compound in a first iteration of a metabolic exploration. Let this value as it is except if you know what you are doing" />\n </section>\n </inputs>\n <outputs>\n- <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />\n- <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" />\n+ <data name="master_pathways" format="csv"\n+ label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />\n+ <data name="compounds" format="tabular"\n+ label="${tool.name} on ${rp2_pathways.name} : Compounds" />\n </outputs>\n <tests>\n <test>\n <!-- test 1: check if identical outputs are produced with default parameters -->\n <param name="rp2_pathways" value="retropath2_pathways.csv" />\n- <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/>\n- <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/>\n+ <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff" />\n+ <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff" />\n </test>\n </tests>\n <help><![CDATA[\n@@ -55,17 +134,6 @@\n \n |\n \n-Input\n------\n-\n-Required information:\n-\n-* **RetroPath2.0 Pathways**\\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis.\n-\n-Advanced options:\n-\n-* **Time Out**\\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes.\n-\n Output\n ------\n \n@@ -73,9 +141,9 @@\n * **Compounds**\\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System).\n ]]></help>\n <creator>\n- <organization name="BioRetroSynth" url="https://github.com/brsynth"/>\n+ <organization name="BioRetroSynth" url="https://github.com/brsynth" />\n </creator>\n <citations>\n <citation type="doi">10.1016/j.ymben.2017.12.002</citation>\n </citations>\n-</tool>\n+</tool>\n\\ No newline at end of file\n' |