| Previous changeset 8:68a5f2db55b9 (2018-11-15) Next changeset 10:2405255d6a09 (2019-02-13) |
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Commit message:
fix cluster file and help section |
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modified:
Marea/local/Recon_rules.p Marea/marea.py Marea/marea.xml Marea/marea_cluster.py Marea/marea_cluster.xml Marea/marea_macros.xml |
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| diff -r 68a5f2db55b9 -r 7c76e8e319c2 Marea/local/Recon_rules.p |
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| Binary file Marea/local/Recon_rules.p has changed |
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| diff -r 68a5f2db55b9 -r 7c76e8e319c2 Marea/marea.py --- a/Marea/marea.py Thu Nov 15 07:36:28 2018 -0500 +++ b/Marea/marea.py Wed Feb 13 04:01:21 2019 -0500 |
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| @@ -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) |
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| diff -r 68a5f2db55b9 -r 7c76e8e319c2 Marea/marea.xml --- a/Marea/marea.xml Thu Nov 15 07:36:28 2018 -0500 +++ b/Marea/marea.xml Wed Feb 13 04:01:21 2019 -0500 |
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| @@ -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> |
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| diff -r 68a5f2db55b9 -r 7c76e8e319c2 Marea/marea_cluster.py --- 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 |
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| @@ -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': |
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| diff -r 68a5f2db55b9 -r 7c76e8e319c2 Marea/marea_macros.xml --- 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 |
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| @@ -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 |