Mercurial > repos > tduigou > rp2paths
changeset 7:4462f4c997ba draft default tip
planemo upload for repository https://github.com/brsynth/rp2paths commit 1a817217fcd199ae61266ec6133137a87f4ab4be-dirty
| author | tduigou |
|---|---|
| date | Fri, 03 Oct 2025 12:18:46 +0000 |
| parents | 016ae4a7705e |
| children | |
| files | rp2paths.xml |
| diffstat | 1 files changed, 90 insertions(+), 22 deletions(-) [+] |
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--- a/rp2paths.xml Wed Jul 24 08:42:00 2024 +0000 +++ b/rp2paths.xml Fri Oct 03 12:18:46 2025 +0000 @@ -1,14 +1,14 @@ <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT"> <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description> <macros> - <token name="@TOOL_VERSION@">1.5.1</token> + <token name="@TOOL_VERSION@">2.1.0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement> </requirements> <stdio> <regex match="TIMEOUT:" level="fatal" /> - <regex match="ERROR:" level="fatal" /> + <regex match="ERROR:" level="fatal" /> <regex match="WARNING:" level="warning" /> </stdio> <command detect_errors="exit_code"><![CDATA[ @@ -16,7 +16,44 @@ python -m rp2paths all '$rp2_pathways' --outdir out - --timeout '$adv.timeout' && + --timeout '$adv.timeout' + #if str($adv.forward) == 'true' + --forward + #end if + #if $adv.cofile + --cofile '$adv.cofile' + #end if + #if str($adv.mindepth) == 'true' + --minDepth + #end if + #if $adv.sink + --customsinkfile '$adv.sink' + #end if + --maxsteps '$adv.maxsteps' + --maxpaths '$adv.maxpaths' + #if str($adv.unfold) == 'true' + --unfold_compounds + #end if + #set cmp_ids = [] + #for $x in $adv.rep_include_path + #silent cmp_ids.append(str($x.cmp_id)) + #end for + #if len(cmp_ids) > 0 + #set cmp_id = ' '.join($cmp_ids) + --onlyPathsStartingBy $cmp_id + #end if + #set cmp_ids = [] + #for $x in $adv.rep_exclude_path + #silent cmp_ids.append(str($x.cmp_id)) + #end for + #if len(cmp_ids) > 0 + #set cmp_id = ' '.join($cmp_ids) + --notPathsStartingBy $cmp_id + #end if + #if $adv.cmpfile + --cmpdnamefile '$adv.cmpfile' + #end if + --target '$adv.target' && mv out/compounds.txt out/compounds.tsv && cp out/compounds.tsv '$compounds' && if test -f 'out/out_paths.csv'; then @@ -24,21 +61,63 @@ fi ]]></command> <inputs> - <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."/> + <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." /> <section name="adv" title="Advanced Options" expanded="false"> - <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." /> + <param name="timeout" type="integer" value="1800" label="Time Out" + help="Time out before killing a process (in seconds), default: 30 minutes." /> + <param + name="forward" type="boolean" checked="false" label="Forward" + help="Consider reactions in the forward direction" /> + <param name="cofile" + type="data" format="csv" optional="True" label="List of cofactors" /> + <param + name="mindepth" type="boolean" checked="false" label="Minimal depth scope" + 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" /> + <param + name="sink" type="data" format="tabular" optional="True" label="List of sinks" + help="Listing compounds to consider as sink compounds. Sink compounds should be provided by their IDs, as used in the reaction.erxn file" /> + <param + name="maxsteps" type="integer" min="0" value="0" max="20" label="Max steps" + help="Cutoff on the maximum number of steps in a pathways. 0 (default) for unlimited number of steps" /> + <param + name="maxpaths" type="integer" min="0" value="0" max="20" label="Max pathways" + help="Cutoff on the maximum number of pathways. 0 (default) for unlimited number of pathways" /> + <param + name="unfold" type="boolean" checked="false" label="Unfold pathways" + help="Unfold pathways based on equivalencie of compounds (can lead to combinatorial explosion)." /> + <repeat name="rep_include_path" title="Include path starting by"> + <param name="cmp_id" type="text" label="Path label" + 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."> + <validator type="empty_field" message="Not empty" /> + </param> + </repeat> + <repeat name="rep_exclude_path" title="Include path starting by"> + <param name="cmp_id" type="text" label="Path label" + help="List of compounds IDs. If specifed, paths making use of one of these compounds as unique initial substrate will be filtered out"> + <validator type="empty_field" message="Not empty" /> + </param> + </repeat> + <param name="cmpfile" type="data" format="tabular" + optional="True" label="List of compounds" help="File with name of compounds" /> + <param + name="target" type="text" value="TARGET_0000000001" + label="Target compound internal ID" + 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" /> </section> </inputs> <outputs> - <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" /> - <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" /> + <data name="master_pathways" format="csv" + label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" /> + <data name="compounds" format="tabular" + label="${tool.name} on ${rp2_pathways.name} : Compounds" /> </outputs> <tests> <test> <!-- test 1: check if identical outputs are produced with default parameters --> <param name="rp2_pathways" value="retropath2_pathways.csv" /> - <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/> - <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/> + <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff" /> + <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff" /> </test> </tests> <help><![CDATA[ @@ -55,17 +134,6 @@ | -Input ------ - -Required information: - -* **RetroPath2.0 Pathways**\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis. - -Advanced options: - -* **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes. - Output ------ @@ -73,9 +141,9 @@ * **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System). ]]></help> <creator> - <organization name="BioRetroSynth" url="https://github.com/brsynth"/> + <organization name="BioRetroSynth" url="https://github.com/brsynth" /> </creator> <citations> <citation type="doi">10.1016/j.ymben.2017.12.002</citation> </citations> -</tool> +</tool> \ No newline at end of file