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comparison deseq2.xml @ 45:702bdf59d6c8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9
author iuc
date Fri, 19 Dec 2025 08:09:31 +0000
parents 1cb33de18af5
children
comparison
equal deleted inserted replaced
44:1cb33de18af5 45:702bdf59d6c8
36 ## This is needed for Pulsar to transfer the file 36 ## This is needed for Pulsar to transfer the file
37 cat '$__tool_directory__/get_deseq_dataset.R' > /dev/null && 37 cat '$__tool_directory__/get_deseq_dataset.R' > /dev/null &&
38 38
39 #import json 39 #import json
40 #import os 40 #import os
41 #import base64
41 Rscript '${__tool_directory__}/deseq2.R' 42 Rscript '${__tool_directory__}/deseq2.R'
42 --cores \${GALAXY_SLOTS:-1} 43 --cores \${GALAXY_SLOTS:-1}
43 -o '$deseq_out' 44 -o '$deseq_out'
44 #if 'pdf' in $output_options.output_selector: 45 #if 'pdf' in $output_options.output_selector:
45 -p '$plots' 46 -p '$plots'
88 #set $count_files = list() 89 #set $count_files = list()
89 #if $select_data.how == 'group_tags': 90 #if $select_data.how == 'group_tags':
90 #for $group in $level.groups.value: 91 #for $group in $level.groups.value:
91 #for $file in $select_data.countsFile.get_datasets_for_group($group): 92 #for $file in $select_data.countsFile.get_datasets_for_group($group):
92 $count_files.append(str($file)) 93 $count_files.append(str($file))
93 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier) 94 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
94 #end for 95 #end for
95 #end for 96 #end for
96 #else: 97 #else:
97 #for $file in $level.countsFile: 98 #for $file in $level.countsFile:
98 $count_files.append(str($file)) 99 $count_files.append(str($file))
99 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier) 100 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
100 #end for 101 #end for
101 #end if 102 #end if
102 $temp_factor.append( {str($level.factorLevel): $count_files} ) 103 $temp_factor.append( {str($level.factorLevel): $count_files} )
103 #end for 104 #end for
104 $temp_factor.reverse() 105 $temp_factor.reverse()
107 #end if 108 #end if
108 109
109 $header 110 $header
110 111
111 #if $select_data.how != 'sample_sheet_contrasts': 112 #if $select_data.how != 'sample_sheet_contrasts':
112 -f '#echo json.dumps(temp_factor_names)#' 113 -f '#echo base64.b64encode(json.dumps(temp_factor_names).encode()).decode()#'
113 #end if 114 #end if
114 -l '#echo json.dumps(filename_to_element_identifiers)#' 115 -l '#echo base64.b64encode(json.dumps(filename_to_element_identifiers).encode()).decode()#'
115 #if $advanced_options.esf_cond.esf: 116 #if $advanced_options.esf_cond.esf:
116 #if $advanced_options.esf_cond.esf == "user": 117 #if $advanced_options.esf_cond.esf == "user":
117 -e $advanced_options.esf_cond.size_factor_input 118 -e $advanced_options.esf_cond.size_factor_input
118 #else: 119 #else:
119 -e $advanced_options.esf_cond.esf 120 -e $advanced_options.esf_cond.esf
152 <option value="datasets_per_level">Select datasets per level</option> 153 <option value="datasets_per_level">Select datasets per level</option>
153 <option value="group_tags">Select group tags corresponding to levels</option> 154 <option value="group_tags">Select group tags corresponding to levels</option>
154 <option value="sample_sheet_contrasts">Select contrasts from sample sheet columns</option> 155 <option value="sample_sheet_contrasts">Select contrasts from sample sheet columns</option>
155 </param> 156 </param>
156 <when value="group_tags"> 157 <when value="group_tags">
157 <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/> 158 <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" />
158 <expand macro="factor_repeat"> 159 <expand macro="factor_repeat">
159 <param name="groups" type="group_tag" data_ref="countsFile" multiple="true" label="Select groups that correspond to this factor level"/> 160 <param name="groups" type="group_tag" data_ref="countsFile" multiple="true" label="Select groups that correspond to this factor level"/>
160 </expand> 161 </expand>
161 </when> 162 </when>
162 <when value="datasets_per_level"> 163 <when value="datasets_per_level">
163 <expand macro="factor_repeat"> 164 <expand macro="factor_repeat">
164 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> 165 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
165 </expand> 166 </expand>
166 </when> 167 </when>
167 <when value="sample_sheet_contrasts"> 168 <when value="sample_sheet_contrasts">
168 <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/> 169 <param name="countsFile" type="data_collection" collection_type="list" format="tabular,tsv" label="Count file(s) collection" />
169 <param name="sample_sheet" type="data" format="tabular" label="Sample sheet file" help="A tabular file containing at least two columns: one with the element identifiers (matching those in the collection) and one or more columns with factor levels."/> 170 <param name="sample_sheet" type="data" format="tabular" label="Sample sheet file" help="A tabular file containing at least two columns: one with the element identifiers (matching those in the collection) and one or more columns with factor levels."/>
170 <conditional name="design_formula_mode"> 171 <conditional name="design_formula_mode">
171 <param name="mode" type="select" label="Design formula specification"> 172 <param name="mode" type="select" label="Design formula specification">
172 <option value="automatic" selected="true">Automatic (select factors from columns)</option> 173 <option value="automatic" selected="true">Automatic (select factors from columns)</option>
173 <option value="custom">Custom design formula</option> 174 <option value="custom">Custom design formula</option>
174 </param> 175 </param>
175 <when value="automatic"> 176 <when value="automatic">
176 <param name="factor" type="data_column" use_header_names="true" data_ref="sample_sheet" multiple="true" optional="false" label="Factor levels column(s)" help="Select one or more columns from the sample sheet to define factor levels for DESeq2 analysis. First selected factor is the primary factor"/> 177 <param name="factor" type="data_column" use_header_names="true" data_ref="sample_sheet" multiple="true" optional="false" label="Factor levels column(s)" help="Select one or more columns from the sample sheet to define factor levels for DESeq2 analysis. First selected factor is the primary factor"/>
177 <param name="reference_level" type="text" label="Reference level for primary factor" help="Specify the reference level for the primary factor. If left blank, the first encountered level of the primary factor will be used as reference." optional="true"/> 178 <expand macro="reference_target_levels"/>
178 <param name="target_level" type="text" label="Target level for primary factor" help="Specify the target level for the primary factor. If left blank, all levels will be compared against the primary factor." optional="true"/>
179 </when> 179 </when>
180 <when value="custom"> 180 <when value="custom">
181 <param name="design_formula" type="text" label="Design formula" help="Specify the design formula using R formula syntax (e.g., '~ condition' or '~ batch + condition'). Column names must match those in the sample sheet. The last factor in the formula is used as the primary factor for contrasts."> 181 <param name="design_formula" type="text" label="Design formula" help="Specify the design formula using R formula syntax (e.g., '~ condition' or '~ batch + condition'). Column names must match those in the sample sheet. The last factor in the formula is used as the primary factor for contrasts.">
182 <validator type="regex" message="Design formula must start with ~ and contain valid R variable names">^~\s*[a-zA-Z][a-zA-Z0-9_.]*(\s*[+*:]\s*[a-zA-Z][a-zA-Z0-9_.]*)*$</validator> 182 <validator type="regex" message="Design formula must start with ~ and contain valid R variable names">^~\s*[a-zA-Z][a-zA-Z0-9_.]*(\s*[+*:]\s*[a-zA-Z][a-zA-Z0-9_.]*)*$</validator>
183 <sanitizer> 183 <sanitizer>
190 <add value="."/> 190 <add value="."/>
191 <add value=" "/> 191 <add value=" "/>
192 </valid> 192 </valid>
193 </sanitizer> 193 </sanitizer>
194 </param> 194 </param>
195 <param name="reference_level" type="text" label="Reference level for primary factor" help="Specify the reference level for the primary factor. If left blank, the first encountered level of the primary factor will be used as reference." optional="true"/> 195 <expand macro="reference_target_levels"/>
196 <param name="target_level" type="text" label="Target level for primary factor" help="Specify the target level for the primary factor. If left blank, all levels will be compared against the primary factor." optional="true"/>
197 </when> 196 </when>
198 </conditional> 197 </conditional>
199 </when> 198 </when>
200 </conditional> 199 </conditional>
201 200