Mercurial > repos > tduigou > rptools_rpscore
annotate rpscore.xml @ 3:e5e66bcdf92b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 162ee89a8e36033f32973d72dfc1b11ca27da61f
author | tduigou |
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date | Fri, 01 Dec 2023 14:29:42 +0000 |
parents | 241da19c48a1 |
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241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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1 <tool id="rptools_rpscore" name="Score Pathway" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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2 <description>Computes a global score for a heterologous pathway</description> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
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3 <macros> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
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4 <import>macros.xml</import> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
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5 </macros> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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6 <expand macro="requirements"/> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
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7 <command detect_errors="exit_code"><![CDATA[ |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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8 python -m rptools.rpscore '$pathway' '$scored_pathway' |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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9 --no_of_rxns_thres '$adv.no_of_rxns_thres' |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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10 --log "error" |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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11 ]]></command> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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12 <inputs> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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13 <param name="pathway" type="data" format="sbml" label="Pathway (rpSBML)" /> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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14 <section name="adv" title="Advanced Options" expanded="false"> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
diff
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15 <param argument="no_of_rxns_thres" type="integer" value="10" label="number of reactions above which a pathway is not scored" /> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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16 </section> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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17 </inputs> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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18 <outputs> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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19 <data name="scored_pathway" format="sbml" label="${tool.name} - ${pathway.name}" /> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
diff
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20 </outputs> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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21 <tests> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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22 <test> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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23 <!-- check if identical outputs are produced with default parameters --> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
diff
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24 <param name="pathway" value="pathway.xml" /> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
diff
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25 <output name="scored_pathway" file="scored_pathway.xml" ftype="sbml" compare="diff" sort="true"/> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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26 </test> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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27 </tests> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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28 <help><![CDATA[ |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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29 Score Pathway |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
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30 ============== |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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31 |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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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. |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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33 |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
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34 Input |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
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35 ----- |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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36 |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
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37 Required: |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
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38 |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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39 * **Pathway (rpSBML)**\ : pathway file (rpSBML) with scores (rules, FBA, Thermo...). |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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40 * **Scored pathway**\ : pathway file (rpSBML) with global score. |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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41 |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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42 Advanced options: |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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43 |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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44 * **--no_of_rxns_thres**\ :(integer, default: 10) Number of reactions above which pathway are not scored |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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45 ]]></help> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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46 <expand macro="creator"/> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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47 <citations> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
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48 <citation type="doi">10.1038/s41467-022-32661-x</citation> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
parents:
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49 </citations> |
241da19c48a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
tduigou
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50 </tool> |