Mercurial > repos > iuc > stacks2_populations
comparison stacks_populations.xml @ 2:38942a7e3801 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4233f68e34f397685885d1828a85d5849a7b17bf"
| author | iuc |
|---|---|
| date | Wed, 12 Feb 2020 18:22:03 -0500 |
| parents | 9a44832748c5 |
| children | b242deb58952 |
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| 1:9a44832748c5 | 2:38942a7e3801 |
|---|---|
| 40 | 40 |
| 41 #if str($popmap) != 'None': | 41 #if str($popmap) != 'None': |
| 42 -M '$popmap' | 42 -M '$popmap' |
| 43 #end if | 43 #end if |
| 44 #if str($batch_size) != '': | 44 #if str($batch_size) != '': |
| 45 -batch_size '$batch_size' | 45 --batch-size '$batch_size' |
| 46 #end if | 46 #end if |
| 47 | 47 |
| 48 ## Data filtering | 48 ## Data filtering |
| 49 | 49 |
| 50 --min-populations $options_filtering.minpop | 50 --min-populations $options_filtering.minpop |
| 307 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> | 307 <element name="catalog.calls.vcf" ftype="vcf" value="gstacks/catalog.calls.vcf" /> |
| 308 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> | 308 <element name="catalog.fa.gz" ftype="fasta.gz" value="gstacks/catalog.fa.gz" /> |
| 309 </collection> | 309 </collection> |
| 310 </param> | 310 </param> |
| 311 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> | 311 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> |
| 312 <param name="batch_size" value="9999" /> | |
| 312 <param name="add_log" value="yes" /> | 313 <param name="add_log" value="yes" /> |
| 313 <output ftype="txt" name="output_log" value="populations/populations.log" lines_diff="4"/> | 314 <output ftype="txt" name="output_log" value="populations/populations.log" lines_diff="4"/> |
| 314 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> | 315 <output ftype="tabular" name="out_haplotypes" value="populations/populations.haplotypes.tsv"/> |
| 315 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/> | 316 <output ftype="tabular" name="out_hapstats" value="populations/populations.hapstats.tsv"/> |
| 316 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/> | 317 <output ftype="txt" name="out_populations_log_distribs" value="populations/populations.log.distribs"/> |