Mercurial > repos > tduigou > rptools_rpscore

comparison rpscore.xml @ 0:241da19c48a1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
author tduigou
date Tue, 28 Mar 2023 12:07:54 +0000
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1 <tool id="rptools_rpscore" name="Score Pathway" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Computes a global score for a heterologous pathway</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 python -m rptools.rpscore '$pathway' '$scored_pathway'
9 --no_of_rxns_thres '$adv.no_of_rxns_thres'
10 --log "error"
11 ]]></command>
12 <inputs>
13 <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" />
14 <section name="adv" title="Advanced Options" expanded="false">
15 <param argument="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" />
16 </section>
17 </inputs>
18 <outputs>
19 <data name="scored_pathway" format="sbml" label="${tool.name} - ${pathway.name}" />
20 </outputs>
21 <tests>
22 <test>
23 <!-- check if identical outputs are produced with default parameters -->
24 <param name="pathway" value="pathway.xml" />
25 <output name="scored_pathway" file="scored_pathway.xml" ftype="sbml" compare="diff" sort="true"/>
26 </test>
27 </tests>
28 <help><![CDATA[
29 Score Pathway
30 ==============
31
32 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.
33
34 Input
35 -----
36
37 Required:
38
39 * **Pathway (rpSBML)**\ : pathway file (rpSBML) with scores (rules, FBA, Thermo...).
40 * **Scored pathway**\ : pathway file (rpSBML) with global score.
41
42 Advanced options:
43
44 * **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored
45 ]]></help>
46 <expand macro="creator"/>
47 <citations>
48 <citation type="doi">10.1038/s41467-022-32661-x</citation>
49 </citations>
50 </tool>