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comparison pvacbind.xml @ 1:747d464670f9 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit 2727330d0394c8a1f178061abffe91fe621be7ee
author galaxyp
date Fri, 12 Dec 2025 21:10:38 +0000
parents 8184d4998259
children
comparison
equal deleted inserted replaced
0:8184d4998259 1:747d464670f9
32 --class-i-epitope-length $class_i_epitope_length 32 --class-i-epitope-length $class_i_epitope_length
33 --class-ii-epitope-length $class_ii_epitope_length 33 --class-ii-epitope-length $class_ii_epitope_length
34 #if $binding_threshold 34 #if $binding_threshold
35 --binding-threshold $binding_threshold 35 --binding-threshold $binding_threshold
36 #end if 36 #end if
37 #if $percentile_threshold_conditional.use_percentile_threshold == "true" 37 #if $percentile_threshold
38 --percentile-threshold $percentile_threshold_conditional.percentile_threshold 38 --percentile-threshold $percentile_threshold
39 --percentile-threshold-strategy $percentile_threshold_conditional.percentile_threshold_strategy 39 #end if
40 #if $percentile_threshold_strategy != 'default'
41 --percentile-threshold-strategy $percentile_threshold_strategy
40 #end if 42 #end if
41 #if $allele_specific_binding_thresholds 43 #if $allele_specific_binding_thresholds
42 --allele-specific-binding-thresholds 44 --allele-specific-binding-thresholds
43 #end if 45 #end if
44 #if $top_score_metric != 'default' 46 #if $top_score_metric != 'default'
142 <option value="28">28</option> 144 <option value="28">28</option>
143 <option value="29">29</option> 145 <option value="29">29</option>
144 <option value="30">30</option> 146 <option value="30">30</option>
145 </param> 147 </param>
146 <param argument="--binding-threshold" type="integer" value="" optional="true" label="Binding Threshold"/> 148 <param argument="--binding-threshold" type="integer" value="" optional="true" label="Binding Threshold"/>
147 <conditional name="percentile_threshold_conditional"> 149 <param argument="--percentile-threshold" type="float" value="" optional="true" label="Percentile Threshold"/>
148 <param name="use_percentile_threshold" type="select" label="Use Percentile Threshold"> 150 <param argument="--percentile-threshold-strategy" type="select" label="Percentile Threshold Strategy">
149 <option value="false" selected="true">No</option> 151 <option value="default" selected="true">Use default</option>
150 <option value="true">Yes</option> 152 <option value="conservative">conservative</option>
151 </param> 153 <option value="exploratory">exploratory</option>
152 <when value="true"> 154 </param>
153 <param argument="--percentile-threshold" type="integer" optional="false" label="Percentile Threshold"/>
154 <param argument="--percentile-threshold-strategy" type="select" label="Percentile Threshold Strategy">
155 <option value="conservative" selected="true">conservative</option>
156 <option value="exploratory">exploratory</option>
157 </param>
158 </when>
159 <when value="false">
160 </when>
161 </conditional>
162 <param argument="--allele-specific-binding-thresholds" type="boolean" checked="false" label="Use allele-specific binding thresholds"/> 155 <param argument="--allele-specific-binding-thresholds" type="boolean" checked="false" label="Use allele-specific binding thresholds"/>
163 <param argument="--top-score-metric" type="select" label="Top Score Metric"> 156 <param argument="--top-score-metric" type="select" label="Top Score Metric">
164 <option value="default" selected="true">Use default</option> 157 <option value="default" selected="true">Use default</option>
165 <option value="lowest">lowest</option> 158 <option value="lowest">lowest</option>
166 <option value="median">median</option> 159 <option value="median">median</option>
189 </param> 182 </param>
190 <param argument="--peptide-fasta" type="data" format="fasta" optional="true" label="Peptide Fasta" help="When running the reference proteome similarity step, use this reference peptide FASTA file to find matches instead of blastp"/> 183 <param argument="--peptide-fasta" type="data" format="fasta" optional="true" label="Peptide Fasta" help="When running the reference proteome similarity step, use this reference peptide FASTA file to find matches instead of blastp"/>
191 <param name="add_sample_name_reports_column" argument="--additional-report-columns" type="boolean" checked="false" label="Add sample name reports column"/> 184 <param name="add_sample_name_reports_column" argument="--additional-report-columns" type="boolean" checked="false" label="Add sample name reports column"/>
192 <param argument="--exclude-NAs" type="boolean" checked="false" label="Exclude NA values from the filtered output"/> 185 <param argument="--exclude-NAs" type="boolean" checked="false" label="Exclude NA values from the filtered output"/>
193 <param argument="--aggregate-inclusion-binding-threshold" type="integer" value="" optional="true" label="Aggregate Inclusion Binding Threshold"/> 186 <param argument="--aggregate-inclusion-binding-threshold" type="integer" value="" optional="true" label="Aggregate Inclusion Binding Threshold"/>
194 <param argument="--aggregate-inclusion-count-limit" type="integer" value="" optional="true" label="Aggregate Inclusion Binding Threshold"/> 187 <param argument="--aggregate-inclusion-count-limit" type="integer" value="" optional="true" label="Aggregate Inclusion Count Limit"/>
195 </inputs> 188 </inputs>
196 189
197 <outputs> 190 <outputs>
198 <collection name="mhc_class_i_outputs" type="list" label="MHC Class I Outputs" > 191 <collection name="mhc_class_i_outputs" type="list" label="MHC Class I Outputs" >
199 <discover_datasets pattern="(?P&lt;designation&gt;.+\.tsv)" ext="tabular" directory="outputs/MHC_Class_I"/> 192 <discover_datasets pattern="(?P&lt;designation&gt;.+\.tsv)" ext="tabular" directory="outputs/MHC_Class_I"/>