Mercurial > repos > tduigou > rptools_rpextractsink

changeset 8:66708fc9c57c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit df6ff93f58dcad0892d429597544cd674f9253ee-dirty
author tduigou
date Thu, 23 Oct 2025 14:40:33 +0000
parents 0ae5837c2e33
children fc1225e0752f
files macros.xml rpextractsink.xml
diffstat 2 files changed, 12 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Oct 22 12:04:01 2025 +0000
+++ b/macros.xml	Thu Oct 23 14:40:33 2025 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">6.6.6</token>
+    <token name="@TOOL_VERSION@">6.7.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
@@ -12,4 +12,4 @@
             <organization name="BioRetroSynth" url="https://github.com/brsynth" />
         </creator>
     </xml>
-</macros>
+</macros>
\ No newline at end of file
--- a/rpextractsink.xml	Wed Oct 22 12:04:01 2025 +0000
+++ b/rpextractsink.xml	Thu Oct 23 14:40:33 2025 +0000
@@ -9,6 +9,14 @@
         <regex match="Could not retreive any species in the compartment" level="fatal" />
     </stdio>
     <command detect_errors="exit_code"><![CDATA[
+        #import os
+        #if "TMPDIR" in os.environ
+            #set tmpdir=os.environ["TMPDIR"]/rr_cache
+            mkdir -p '$tmpdir' &&
+        #else
+            #set tmpdir="."
+        #end if
+
         python -m rptools.rpextractsink
             '$input'
             '$sink'
@@ -16,6 +24,7 @@
             $adv.remove_dead_end
             $adv.standalone
             --chemical-space '$adv.datatype'
+            --cache-dir '$tmpdir'
     ]]></command>
     <inputs>
         <param name="input" type="data" format="sbml" optional="false" label="Strain"
@@ -58,19 +67,6 @@
 
 The results are written to a RetroPath2.0 friendly CSV file format that can be used as sink input.
 
-Input
------
-
-Required:
-
-* **Strain**\ : The structure of metabolites present in the chosen chassis strain in SBML format.
-* **SBML compartment ID**\ : (string, default: c) Specify the compartment from which to extract the sink molecules. The default are for BiGG models (cytosol).
-
-Advanced options:
-
-* **Remove dead-end metabolites using FVA evaluation?**\ : (boolean, default: True) Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites.
-* **Do not connect to Internet**: (boolean, default: False) If True, do not retrieve InChI from Internet
-
 Output
 ------
 
@@ -83,4 +79,4 @@
         <citation type="doi">10.1186/1752-0509-7-74</citation>
         <citation type="doi">10.1038/s41467-022-32661-x</citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file