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comparison lumpy.xml @ 3:da5aae7550b3 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 810390d1104d08df5cf35d501b50650455b99684"
author artbio
date Thu, 07 May 2020 19:38:14 -0400
parents 6059f4cb4cf2
children 093bb151a0a8
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2:6059f4cb4cf2 3:da5aae7550b3
1 <tool id="lumpy" name="lumpy-sv" version="1.1.0"> 1 <tool id="lumpy" name="lumpy-sv" version="1.2.0">
2 <description>find structural variants</description> 2 <description>find structural variants</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.13">lumpy-sv</requirement> 4 <requirement type="package" version="0.2.13">lumpy-sv</requirement>
5 <requirement type="package" version="1.3.1">samtools</requirement> 5 <requirement type="package" version="1.3.1">samtools</requirement>
6 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> 6 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
151 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> 151 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
152 </data> 152 </data>
153 <data format="bam" name="discordants" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.bam"> 153 <data format="bam" name="discordants" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.bam">
154 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 154 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
155 </data> 155 </data>
156 <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.B.bam"> 156 <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.B.discordants.bam">
157 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 157 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
158 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> 158 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
159 </data> 159 </data>
160 <data format="vcf" name="vcf_call" label="Lumpy Variant Calling"> 160 <data format="vcf" name="vcf_call" label="Lumpy Variant Calling">
161 <change_format> 161 <change_format>
163 </change_format> 163 </change_format>
164 </data> 164 </data>
165 </outputs> 165 </outputs>
166 166
167 <tests> 167 <tests>
168 <test>
169 <param name="analysis_type_list" value="two_sample" />
170 <param name="input_file" value="sample_Del.bam" ftype="bam"/>
171 <param name="input_fileB" value="sample_cle.bam" ftype="bam"/>
172 <param name="seq_method_list" value="paired-end" />
173 <param name="mw" value="4"/>
174 <param name="tt" value="0"/>
175 <param name="back_distance" value="10"/>
176 <param name="weight" value="1" />
177 <param name="min_mapping_threshold" value="20" />
178 <output name="vcf_call" file="output_two.paired_end.vcf" ftype="vcf"/>
179 </test>
168 <test> 180 <test>
169 <param name="analysis_type_list" value="one_sample" /> 181 <param name="analysis_type_list" value="one_sample" />
170 <param name="input_file" value="sr.input.bam" ftype="bam"/> 182 <param name="input_file" value="sr.input.bam" ftype="bam"/>
171 <param name="seq_method_list" value="single-read" /> 183 <param name="seq_method_list" value="single-read" />
172 <param name="mw" value="4"/> 184 <param name="mw" value="4"/>