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changeset 9:7c76e8e319c2 draft

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fix cluster file and help section
author bimib
date Wed, 13 Feb 2019 04:01:21 -0500
parents 68a5f2db55b9
children 2405255d6a09
files Marea/local/Recon_rules.p Marea/marea.py Marea/marea.xml Marea/marea_cluster.py Marea/marea_cluster.xml Marea/marea_macros.xml
diffstat 5 files changed, 10 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
Binary file Marea/local/Recon_rules.p has changed
--- a/Marea/marea.py	Thu Nov 15 07:36:28 2018 -0500
+++ b/Marea/marea.py	Wed Feb 13 04:01:21 2019 -0500
@@ -456,7 +456,7 @@
                 elif l[0] == 'or':
                     flag = False
                     break
-            if flag == True: #se ci sono solo AND nella lista
+            if flag == True: #when there are only AND in list
                 tmp.extend(tmpAnd)
             elif flag == False:
                 tmp.append(tmpAnd)
--- a/Marea/marea.xml	Thu Nov 15 07:36:28 2018 -0500
+++ b/Marea/marea.xml	Wed Feb 13 04:01:21 2019 -0500
@@ -83,8 +83,8 @@
             </when>
         </conditional>
         <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 
-        <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold" help="min value 0" />
-        <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold" help="min value 1" />
+        <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" />
+        <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold:" help="min value 1" />
     </inputs>
 
     <outputs>
--- a/Marea/marea_cluster.py	Thu Nov 15 07:36:28 2018 -0500
+++ b/Marea/marea_cluster.py	Wed Feb 13 04:01:21 2019 -0500
@@ -577,7 +577,12 @@
 def main():
     args = process_args(sys.argv)
     if args.k_min > args.k_max:
-        sys.exit('Execution aborted: max cluster > min cluster')
+         warning('k range boundaries inverted.')
+         tmp = args.k_min
+         args.k_min = args.k_max
+         args.k_max = tmp
+    else: 
+        warning('k range correct.')
     if args.rules_selector == 'HMRcore':
         recon = pk.load(open(args.tool_dir + '/local/HMRcore_rules.p', 'rb'))
     elif args.rules_selector == 'Recon':
--- a/Marea/marea_macros.xml	Thu Nov 15 07:36:28 2018 -0500
+++ b/Marea/marea_macros.xml	Wed Feb 13 04:01:21 2019 -0500
@@ -66,7 +66,7 @@
 
     <token name="@REFERENCE@">
 
-This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_. Development team: Irene Sala, Luca Rosato, Davide Maspero, Chiara Damiani.
+This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_.
 
 .. _BIMIB: http://sito di bio.org
 .. _Department of Informatics, Systems and Communications: http://www.disco.unimib.it/go/Home/English