diff --git a/biobb_dna/backbone/bipopulations.py b/biobb_dna/backbone/bipopulations.py index c383d9a0..54814df7 100755 --- a/biobb_dna/backbone/bipopulations.py +++ b/biobb_dna/backbone/bipopulations.py @@ -31,6 +31,7 @@ class BIPopulations(BiobbObject): * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze. If not specified it will analyse the complete sequence. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/backbone/canonicalag.py b/biobb_dna/backbone/canonicalag.py index 89df92a5..8e7a8e01 100755 --- a/biobb_dna/backbone/canonicalag.py +++ b/biobb_dna/backbone/canonicalag.py @@ -31,6 +31,7 @@ class CanonicalAG(BiobbObject): * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze. If not specified it will analyse the complete sequence. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/backbone/puckering.py b/biobb_dna/backbone/puckering.py index 930edfa3..ac4973e3 100755 --- a/biobb_dna/backbone/puckering.py +++ b/biobb_dna/backbone/puckering.py @@ -30,6 +30,7 @@ class Puckering(BiobbObject): * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze. If not specified it will analyse the complete sequence. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/curvesplus/biobb_canal.py b/biobb_dna/curvesplus/biobb_canal.py index 94468d61..58e1ecb3 100755 --- a/biobb_dna/curvesplus/biobb_canal.py +++ b/biobb_dna/curvesplus/biobb_canal.py @@ -38,6 +38,7 @@ class Canal(BiobbObject): * **binary_path** (*str*) - ('Canal') Path to Canal executable, otherwise the program wil look for Canal executable in the binaries folder. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/curvesplus/biobb_canion.py b/biobb_dna/curvesplus/biobb_canion.py index 4be5ba55..917e5e43 100755 --- a/biobb_dna/curvesplus/biobb_canion.py +++ b/biobb_dna/curvesplus/biobb_canion.py @@ -39,6 +39,7 @@ class Canion(BiobbObject): * **binary_path** (*str*) - (Canion) Path to Canion executable, otherwise the program wil look for Canion executable in the binaries folder. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/curvesplus/biobb_curves.py b/biobb_dna/curvesplus/biobb_curves.py index a5edd83f..780b619a 100755 --- a/biobb_dna/curvesplus/biobb_curves.py +++ b/biobb_dna/curvesplus/biobb_curves.py @@ -39,6 +39,7 @@ class Curves(BiobbObject): * **binary_path** (*str*) - (Cur+) Path to Curves+ executable, otherwise the program wil look for Cur+ executable in the binaries folder. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/dna/dna_averages.py b/biobb_dna/dna/dna_averages.py index 0eb61726..0ad1d0ce 100755 --- a/biobb_dna/dna/dna_averages.py +++ b/biobb_dna/dna/dna_averages.py @@ -30,6 +30,7 @@ class HelParAverages(BiobbObject): * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze. If not specified it will analyse the complete sequence. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/dna/dna_bimodality.py b/biobb_dna/dna/dna_bimodality.py index b9d0382b..4b76d2f8 100755 --- a/biobb_dna/dna/dna_bimodality.py +++ b/biobb_dna/dna/dna_bimodality.py @@ -35,7 +35,8 @@ class HelParBimodality(BiobbObject): * **max_iter** (*int*) - (400) Number of maximum iterations for EM algorithm. * **tol** (*float*) - (1e-5) Tolerance value for EM algorithm. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. - * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.1 + * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.1 Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/dna/dna_timeseries.py b/biobb_dna/dna/dna_timeseries.py index 35204b75..b0556b99 100755 --- a/biobb_dna/dna/dna_timeseries.py +++ b/biobb_dna/dna/dna_timeseries.py @@ -32,6 +32,7 @@ class HelParTimeSeries(BiobbObject): * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze. If not specified it will analyse the complete sequence. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/interbp_correlations/interbpcorr.py b/biobb_dna/interbp_correlations/interbpcorr.py index 8429ab41..bf72bfb4 100755 --- a/biobb_dna/interbp_correlations/interbpcorr.py +++ b/biobb_dna/interbp_correlations/interbpcorr.py @@ -36,6 +36,7 @@ class InterBasePairCorrelation(BiobbObject): * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze. If not specified it will analyse the complete sequence. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/interbp_correlations/interhpcorr.py b/biobb_dna/interbp_correlations/interhpcorr.py index 875f6c8a..11240119 100755 --- a/biobb_dna/interbp_correlations/interhpcorr.py +++ b/biobb_dna/interbp_correlations/interhpcorr.py @@ -32,6 +32,8 @@ class InterHelParCorrelation(BiobbObject): * **basepair** (*str*) - (None) Name of basepair analyzed. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. + * **basepair** (*str*) - (None) Name of basepair analyzed. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/interbp_correlations/interseqcorr.py b/biobb_dna/interbp_correlations/interseqcorr.py index cfa561ea..f0206bba 100755 --- a/biobb_dna/interbp_correlations/interseqcorr.py +++ b/biobb_dna/interbp_correlations/interseqcorr.py @@ -30,6 +30,7 @@ class InterSequenceCorrelation(BiobbObject): * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze. If not specified it will analyse the complete sequence. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/intrabp_correlations/intrabpcorr.py b/biobb_dna/intrabp_correlations/intrabpcorr.py index e78b2f05..7cf3cbc7 100755 --- a/biobb_dna/intrabp_correlations/intrabpcorr.py +++ b/biobb_dna/intrabp_correlations/intrabpcorr.py @@ -36,6 +36,7 @@ class IntraBasePairCorrelation(BiobbObject): * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze. If not specified it will analyse the complete sequence. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/intrabp_correlations/intrahpcorr.py b/biobb_dna/intrabp_correlations/intrahpcorr.py index 83976f0c..72204e98 100755 --- a/biobb_dna/intrabp_correlations/intrahpcorr.py +++ b/biobb_dna/intrabp_correlations/intrahpcorr.py @@ -32,6 +32,8 @@ class IntraHelParCorrelation(BiobbObject): * **base** (*str*) - (None) Name of base analyzed. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. + * **base** (*str*) - (None) Name of base analyzed. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/intrabp_correlations/intraseqcorr.py b/biobb_dna/intrabp_correlations/intraseqcorr.py index b38e0531..36c54635 100755 --- a/biobb_dna/intrabp_correlations/intraseqcorr.py +++ b/biobb_dna/intrabp_correlations/intraseqcorr.py @@ -30,6 +30,7 @@ class IntraSequenceCorrelation(BiobbObject): * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze. If not specified it will analyse the complete sequence. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/stiffness/average_stiffness.py b/biobb_dna/stiffness/average_stiffness.py index d473af37..21e6badf 100755 --- a/biobb_dna/stiffness/average_stiffness.py +++ b/biobb_dna/stiffness/average_stiffness.py @@ -31,6 +31,7 @@ class AverageStiffness(BiobbObject): * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze. If not specified it will analyse the complete sequence. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python:: diff --git a/biobb_dna/stiffness/basepair_stiffness.py b/biobb_dna/stiffness/basepair_stiffness.py index aac015e4..f5f74ace 100755 --- a/biobb_dna/stiffness/basepair_stiffness.py +++ b/biobb_dna/stiffness/basepair_stiffness.py @@ -34,6 +34,7 @@ class BPStiffness(BiobbObject): * **scaling** (*list*) - ([1, 1, 1, 10.6, 10.6, 10.6]) Values by which to scale stiffness. Positions correspond to helical parameters in the order: shift, slide, rise, tilt, roll, twist. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. + * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. Examples: This is a use example of how to use the building block from Python::