changeset 13:7aa851f87974 draft

Uploaded
author pavanvidem
date Mon, 31 Aug 2015 09:23:45 -0400
parents cbd118202fd1
children a6949dd64d9c
files dexseq.xml dexseq_helper.py tool_dependencies.xml
diffstat 3 files changed, 8 insertions(+), 65 deletions(-) [+]
line wrap: on
line diff
--- 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 @@
 <tool id="dexseq" name="DEXSeq" version="1.0">
     <description>Determines differentially expressed features from count tables</description>
     <requirements>
-        <requirement type="package" version="3.1.2">R</requirement>
+        <requirement type="package" version="3.2.0">R</requirement>
         <requirement type="binary">Rscript</requirement>
-        <requirement type="package" version="1.6.1">deseq2</requirement>
-        <requirement type="R-module">DESeq2</requirement>
+        <requirement type="package" version="1.14.2">DEXSeq</requirement>
     </requirements>
     <code file="dexseq_helper.py" />
     <command>
         #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:
--- 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.'
+
--- 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 @@
                     <repository changeset_revision="d973c8e9b29e" name="package_r_3_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="R" version="3.2.0" />
                     </repository>
+                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/getopt_1.20.0.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/lambda.r_1.1.7.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/futile.options_1.0.0.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/futile.logger_1.4.1.tar.gz</package>