# HG changeset patch # User pavanvidem # Date 1441027425 14400 # Node ID 7aa851f87974ba812f65bddaa4a44402ffa40d6f # Parent cbd118202fd1103bbaf984ec35525d264d23d8b2 Uploaded diff -r cbd118202fd1 -r 7aa851f87974 dexseq.xml --- a/dexseq.xml Mon Aug 31 06:19:57 2015 -0400 +++ b/dexseq.xml Mon Aug 31 09:23:45 2015 -0400 @@ -1,17 +1,16 @@ Determines differentially expressed features from count tables - R + R Rscript - deseq2 - DESeq2 + DEXSeq #import json - Rscript /usr/local/galaxy/galaxy-dist/tools/test/deseq2/dexseq.R - #set $reportdir = $deseq_out.files_path - -o "$deseq_out" + Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/pavanvidem/dexseq/cbd118202fd1/dexseq/dexseq.R + #set $reportdir = $dexseq_out.files_path + -o "$dexseq_out" -p 12 #set $temp_factor_names = list() #for $factor in $rep_factorName: diff -r cbd118202fd1 -r 7aa851f87974 dexseq_helper.py --- a/dexseq_helper.py Mon Aug 31 06:19:57 2015 -0400 +++ b/dexseq_helper.py Mon Aug 31 09:23:45 2015 -0400 @@ -1,29 +1,6 @@ from galaxy.tools.parameters import DataToolParameter -def get_matrix_header( input_dataset ): - """ - Not used currently, because the reload of the ckeckboxes did not work. - """ - input_handle = open( input_dataset.file_name ) - first_header = input_handle.readline() - second_header = input_handle.readline() - return [('%s::%s' % (cname2,cname1), str(int(col_num) + 1), False) for col_num, (cname2, cname1) in enumerate(zip(second_header.split()[1:],first_header.split()[1:])) ] - - - -def _construct_error_map( error_map, rep_dict, rep_parent, child, error_value ): - """ - Its no so easy to create a propper error_map for repetitions in Galaxy. - This is a helper function. - """ - - error_map[ rep_parent ] = [ dict() for t in rep_dict ] - for i in range( len( rep_dict ) ): - error_map[ rep_parent ][i][ child ] = error_value - - - def validate_input( trans, error_map, param_values, page_param_map ): """ Validates the user input, before execution. @@ -32,10 +9,6 @@ factor_name_list = [] factor_duplication = False level_duplication = False - overlapping_selection = False - - first_condition = True - factor_indieces = list() for factor in factors: # factor names should be unique @@ -48,10 +21,6 @@ level_name_list = list() factor_index_list = list() - if first_condition and len( factor['rep_factorLevel'] ) < 2: - # first condition needs to have at least 2 levels - _construct_error_map( error_map, factors, 'rep_factorName', 'rep_factorLevel', [ {'factorLevel': 'The first condition should have at least 2 factor'} for t in factor['rep_factorLevel'] ] ) - for level in factor['rep_factorLevel']: # level names under one factor should be unique fl = level['factorLevel'] @@ -59,40 +28,14 @@ level_duplication = True level_name_list.append( fl ) - fi = level['factorIndex'] - if fi: - # the checkboxes should not have an overlap - for check in fi: - if check in factor_index_list: - overlapping_selection = True - factor_index_list.append( check ) - - print set(factor_index_list) - print factor_indieces - if set(factor_index_list) in factor_indieces: - _construct_error_map( error_map, factors, 'rep_factorName', 'rep_factorLevel', [ {'factorLevel': 'It is not allowed to have two identical factors, that means two factors with the same toggeled checked boxes. '} for t in factor['rep_factorLevel'] ] ) - else: - factor_indieces.append( set(factor_index_list) ) - - - if level_duplication: error_map['rep_factorName'] = [ dict() for t in factors ] for i in range( len( factors ) ): error_map['rep_factorName'][i]['rep_factorLevel'] = [ {'factorLevel': 'Factor levels for each factor need to be unique'} for t in factor['rep_factorLevel'] ] break - if overlapping_selection: - error_map['rep_factorName'] = [ dict() for t in factors ] - for i in range( len( factors ) ): - error_map['rep_factorName'][i]['rep_factorLevel'] = [ {'factorIndex': 'The samples from different factors are not allowed to overlap'} for t in factor['rep_factorLevel'] ] - break - - first_condition = False if factor_duplication: - _construct_error_map( error_map, factors, 'rep_factorName', 'factorName', 'Factor names need to be unique' ) - """ error_map['rep_factorName'] = [ dict() for t in factors ] for i in range( len( factors ) ): - error_map['rep_factorName'][i]['factorName'] = 'Factor names need to be unique' - """ + error_map['rep_factorName'][i]['factorName'] = 'Factor names need to be unique.' + diff -r cbd118202fd1 -r 7aa851f87974 tool_dependencies.xml --- a/tool_dependencies.xml Mon Aug 31 06:19:57 2015 -0400 +++ b/tool_dependencies.xml Mon Aug 31 09:23:45 2015 -0400 @@ -10,6 +10,7 @@ + https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/getopt_1.20.0.tar.gz https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/lambda.r_1.1.7.tar.gz https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/futile.options_1.0.0.tar.gz https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/futile.logger_1.4.1.tar.gz