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comparison picard_MergeBamAlignment.xml @ 31:585027e65f3b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 70d2a66c405be58d4413753792bcadf212a4da84
author iuc
date Sat, 25 Feb 2023 20:33:49 +0000
parents 2a17c789e0a5
children f9242e01365a
comparison
equal deleted inserted replaced
30:b502c227b5e6 31:585027e65f3b
1 <tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>merge alignment data with additional info stored in an unmapped BAM dataset</description> 2 <description>merge alignment data with additional info stored in an unmapped BAM dataset</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">1</token> 5 <token name="@WRAPPER_VERSION@">2</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @java_options@ 9 @java_options@
10 #set $picard_dict = "localref.dict" 10 #set $picard_dict = "localref.dict"
174 <param name="include_secondary_alignments" type="boolean" checked="True" label="If false, do not write secondary alignments to output" help="INCLUDE_SECONDARY_ALIGNMENTS; default=True"/> 174 <param name="include_secondary_alignments" type="boolean" checked="True" label="If false, do not write secondary alignments to output" help="INCLUDE_SECONDARY_ALIGNMENTS; default=True"/>
175 <param name="add_mate_cigar" type="boolean" checked="True" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/> 175 <param name="add_mate_cigar" type="boolean" checked="True" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
176 <expand macro="VS" /> 176 <expand macro="VS" />
177 </inputs> 177 </inputs>
178 <outputs> 178 <outputs>
179 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with merged alignments"/> 179 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM"/>
180 </outputs> 180 </outputs>
181 <tests> 181 <tests>
182 <test> 182 <test>
183 <param name="reference_source_selector" value="history" /> 183 <param name="reference_source_selector" value="history" />
184 <param name="ref_file" value="picard_MergeBamAlignment_ref.fa" ftype="fasta" /> 184 <param name="ref_file" value="picard_MergeBamAlignment_ref.fa" ftype="fasta" />
189 <param name="is_bisulfite_sequence" value="False"/> 189 <param name="is_bisulfite_sequence" value="False"/>
190 <param name="aligned_reads_only" value="False"/> 190 <param name="aligned_reads_only" value="False"/>
191 <param name="max_insertions_or_deletions" value="1"/> 191 <param name="max_insertions_or_deletions" value="1"/>
192 <param name="read1_trim" value="0"/> 192 <param name="read1_trim" value="0"/>
193 <param name="read2_trim" value="0"/> 193 <param name="read2_trim" value="0"/>
194 <param name="orientation" value="FR"/> 194 <param name="orientations" value="FR"/>
195 <param name="aligner_proper_pair_flags" value="False"/> 195 <param name="aligner_proper_pair_flags" value="False"/>
196 <param name="primary_alignment_strategy" value="BestMapq"/> 196 <param name="primary_alignment_strategy" value="BestMapq"/>
197 <param name="clip_overlapping_reads" value="True"/> 197 <param name="clip_overlapping_reads" value="True"/>
198 <param name="include_secondary_alignments" value="True"/> 198 <param name="include_secondary_alignments" value="True"/>
199 <param name="add_mate_cigar" value="True"/> 199 <param name="add_mate_cigar" value="True"/>