Mercurial > repos > artbio > lumpy_sv
comparison lumpy.xml @ 3:da5aae7550b3 draft
"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"/> |