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comparison rnachipintegrator_wrapper.xml @ 6:466c68008537 draft default tip

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Updated for RnaChipIntegrator 3.0.0.
author pjbriggs
date Wed, 20 Mar 2024 09:11:04 +0000
parents b695071de766
children
comparison
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5:087d9872fb0d 6:466c68008537
4 <macros> 4 <macros>
5 <import>rnachipintegrator_macros.xml</import> 5 <import>rnachipintegrator_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command interpreter="bash"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 rnachipintegrator_wrapper.sh 10 bash $__tool_directory__/rnachipintegrator_wrapper.sh
11 #if $peaks_in.metadata.chromCol 11 #if $peaks_in.metadata.chromCol
12 --peak_cols=${peaks_in.metadata.chromCol},${peaks_in.metadata.startCol},${peaks_in.metadata.endCol} 12 --peak_cols=${peaks_in.metadata.chromCol},${peaks_in.metadata.startCol},${peaks_in.metadata.endCol}
13 #end if 13 #end if
14 #if str( $cutoff ) != "" 14 #if str( $cutoff ) != ""
15 --cutoff=$cutoff 15 --cutoff=$cutoff
164 <output name="peaks_per_feature_summary" ftype="tabular" 164 <output name="peaks_per_feature_summary" ftype="tabular"
165 file="peaks_per_feature6.summary" /> 165 file="peaks_per_feature6.summary" />
166 <output name="features_per_peak_summary" ftype="tabular" 166 <output name="features_per_peak_summary" ftype="tabular"
167 file="features_per_peak6.summary" /> 167 file="features_per_peak6.summary" />
168 </test> 168 </test>
169 <!--
170 RnaChipIntegrator +name=test +cutoff=130000 +edge=tes +xlsx features.txt peaks.txt
171 -->
172 <test>
173 <param name="features_in" value="features.txt" ftype="tabular" />
174 <param name="peaks_in" value="peaks.txt" ftype="tabular" />
175 <param name="cutoff" value="130000" />
176 <param name="edge" value="tes" />
177 <output name="xlsx_out" file="peaks7.xlsx" compare="sim_size" />
178 <output name="peaks_per_feature_out" ftype="tabular"
179 file="peaks_per_feature7.out" />
180 <output name="features_per_peak_out" ftype="tabular"
181 file="features_per_peak7.out" />
182 </test>
169 </tests> 183 </tests>
170 <help> 184 <help>
171 185
172 .. class:: infomark 186 .. class:: infomark
173 187