Mercurial > repos > tduigou > rpscore

changeset 1:da8ae7fa5ed3 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Thu, 10 Feb 2022 12:17:38 +0000
parents f818d489ca7d
children eddae32301bd
files rpscore.xml wrap.xml
diffstat 2 files changed, 66 insertions(+), 71 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpscore.xml	Thu Feb 10 12:17:38 2022 +0000
@@ -0,0 +1,66 @@
+<tool id="rpscore" name="Score Pathway" version="@TOOL_VERSION@" profile="19.09">
+    <description>Computes a global score for a heterologous pathway.</description>
+    <macros>
+        <token name="@TOOL_VERSION@">5.12.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m rptools.rpscore '$pathway' '$scored_pathway'
+        --no_of_rxns_thres '$adv.no_of_rxns_thres'
+        --log "error"
+    ]]></command>
+    <inputs>
+        <param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="scored_pathway" format="xml" label="${tool.name} - ${pathway.name}" />
+    </outputs>
+    <tests>
+        <test>
+        <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <param name="pathway" value="pathway.xml" />
+            <output name="scored_pathway" file="scored_pathway.xml" ftype="xml" compare="diff" sort="true"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+rpscore
+=========
+
+
+Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway.
+
+
+Input
+-----
+
+Required:
+
+* **infile**\ : (string) Pathway file (rpSBML) with scores (rules, FBA, Thermo...)
+* **outfile**\ : (string) Path to write pathway file (rpSBML) with global score
+
+Advanced options:
+
+* **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored (too long)
+
+Version
+----------
+
+5.12.1
+
+Authors
+-------
+
+* **Jean-Loup Faulon**
+* **Joan Hérisson**
+
+Acknowledgments
+---------------
+
+* Thomas Duigou
+    ]]></help>
+</tool>
\ No newline at end of file
--- a/wrap.xml	Tue Dec 07 15:53:15 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-<tool id="rpscore" name="Score Pathway" version="5.9.2">
-    <description>Computes a global score for a heterologous pathway.</description>
-	<requirements>
-        <requirement type="package" version="5.9.2">rptools</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-	    python -m rptools.rpscore '$pathway' '$scored_pathway'
-        --no_of_rxns_thres '$adv.no_of_rxns_thres'
-        --log '$adv.log_level'
-    ]]></command>
-    <inputs>
-		<param name="pathway" type="data" format="xml" label="Pathway (rpSBML)" />
-		<section name="adv" title="Advanced Options" expanded="false">
-            <param name="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
-			<param name="log_level"      type="select"  label="Log level">
-                <option value="debug"                    >debug</option>
-                <option value="info"                     >info</option>
-			    <option value="warning"                  >warning</option>
-			    <option value="error"     selected="true">error</option>
-			    <option value="critical"                 >critical</option>
-            </param>
-		</section>
-    </inputs>
-    <outputs>
-        <data name="scored_pathway" format="xml" label="${tool.name} - ${pathway.name}" />
-    </outputs>
-    <tests>
-        <test>
-        <!-- test 1: check if identical outputs are produced with default parameters  -->
-            <param name="pathway" value="pathway.xml" />
-            <output name="scored_pathway" file="scored_pathway.xml" ftype="xml" compare="diff" sort="true"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-rpscore
-=========
-
-
-Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway.
-
-
-Input
------
-
-Required:
-
-* **infile**\ : (string) Pathway file (rpSBML) with scores (rules, FBA, Thermo...)
-* **outfile**\ : (string) Path to write pathway file (rpSBML) with global score
-
-Advanced options:
-
-* **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored (too long)
-* **--log**: (string, default=error) Set the log level, choices are 'debug', 'info', 'warning', 'error', 'critical'
-
-Version
-----------
-
-5.9.2
-
-Authors
--------
-
-* **Jean-Loup Faulon**
-* **Joan Hérisson**
-
-Acknowledgments
----------------
-
-* Thomas Duigou
-    ]]></help>
-</tool>
\ No newline at end of file