Mercurial > repos > sanbi-uwc > shapeit_phase
comparison shapeit_phase.xml @ 16:1a00583b6b2c draft
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
| author | sanbi-uwc |
|---|---|
| date | Tue, 18 Sep 2018 08:48:52 -0400 |
| parents | 201d098d6d67 |
| children | 1f460ad509b6 |
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| 15:201d098d6d67 | 16:1a00583b6b2c |
|---|---|
| 1 <tool id="shapeit_phase" name="shapeit_phase" version="0.14.0"> | 1 <tool id="shapeit_phase" name="shapeit_phase" version="0.15.0"> |
| 2 <description>genomic data with or without reference panel</description> | 2 <description>genomic data with or without reference panel</description> |
| 3 | |
| 4 <requirements> | 3 <requirements> |
| 5 <requirement type="package" version="2.r837">shapeit</requirement> | 4 <requirement type="package" version="2.r837">shapeit</requirement> |
| 6 </requirements> | 5 </requirements> |
| 7 <stdio> | 6 <stdio> |
| 8 <exit_code range="1:" /> | 7 <exit_code range="1:" /> |
| 60 #end for | 59 #end for |
| 61 #end if | 60 #end if |
| 62 | 61 |
| 63 shapeit | 62 shapeit |
| 64 | 63 |
| 64 #if $check_mode != "": | |
| 65 -check | |
| 66 #end if | |
| 67 | |
| 65 #if $input_files.input_type_select == "vcf": | 68 #if $input_files.input_type_select == "vcf": |
| 66 --input-vcf ${input_files.vcf_file} | 69 --input-vcf ${input_files.vcf_file} |
| 67 #else if $input_files.input_type_select == "plink_ped_map": | 70 #else if $input_files.input_type_select == "plink_ped_map": |
| 68 --input-ped ${input_files.plink_ped} ${input_files.plink_map} | 71 --input-ped ${input_files.plink_ped} ${input_files.plink_map} |
| 69 #if $input_files.plink_missing_code != "0": | 72 #if $input_files.plink_missing_code != "0": |
| 170 #end if | 173 #end if |
| 171 #if $use_advanced_parameters.set_rng_seed.set_rng_seed_select == "set_rng_seed_yes": | 174 #if $use_advanced_parameters.set_rng_seed.set_rng_seed_select == "set_rng_seed_yes": |
| 172 --seed $use_advanced_parameters.rng_seed | 175 --seed $use_advanced_parameters.rng_seed |
| 173 #end if | 176 #end if |
| 174 #end if | 177 #end if |
| 175 --output-max $out_haps $out_sample | 178 |
| 176 --output-graph $out_graph | 179 #if $check_mode == "": |
| 177 --output-log $out_log | 180 --output-max $out_haps $out_sample |
| 181 --output-graph $out_graph | |
| 182 --output-log $out_log | |
| 183 #else | |
| 184 --output-log output | |
| 185 && mv output.mendel.log $out_log | |
| 186 && mv output.mendel.snp.strand $out_strand | |
| 187 && mv output.mendel.snp.strand.exclude $out_exclude | |
| 188 #end if | |
| 178 ]]></command> | 189 ]]></command> |
| 179 | 190 |
| 180 <inputs> | 191 <inputs> |
| 192 <param name="check_mode" type="boolean" truevalue="-check" falsevalue="" label="Run in -check mode (check data)" /> | |
| 181 <conditional name="input_files"> | 193 <conditional name="input_files"> |
| 182 <param name="input_type_select" type="select" label="Please specify your input files."> | 194 <param name="input_type_select" type="select" label="Please specify your input files."> |
| 183 <option value="vcf" selected="True">VCF Variant Call Format</option> | 195 <option value="vcf" selected="True">VCF Variant Call Format</option> |
| 184 <option value="plink_ped_map">Plink PED/MAP format</option> | 196 <option value="plink_ped_map">Plink PED/MAP format</option> |
| 185 <option value="plink_bed_bim_fam">Plink BED/BIM/FAM format</option> | 197 <option value="plink_bed_bim_fam">Plink BED/BIM/FAM format</option> |
| 428 <when value="use_filters_no"></when> | 440 <when value="use_filters_no"></when> |
| 429 </conditional> | 441 </conditional> |
| 430 | 442 |
| 431 </inputs> | 443 </inputs> |
| 432 <outputs> | 444 <outputs> |
| 433 <data name="out_haps" format="tabular" label="${tool.name} on ${on_string} haplotypes (.haps)"/> | 445 <data name="out_haps" format="tabular" label="${tool.name} on ${on_string} haplotypes (.haps)"> |
| 434 <data name="out_sample" format="tabular" label="${tool.name} on ${on_string} additional information (.sample)"/> | 446 <filter>not check_mode</filter> |
| 435 <data name="out_graph" format="txt" label="${tool.name} on ${on_string} haplotype graphs (.hgraph)"/> | 447 </data> |
| 448 <data name="out_sample" format="tabular" label="${tool.name} on ${on_string} additional information (.sample)"> | |
| 449 <filter>not check_mode</filter> | |
| 450 </data> | |
| 451 <data name="out_graph" format="txt" label="${tool.name} on ${on_string} haplotype graphs (.hgraph)"> | |
| 452 <filter>not check_mode</filter> | |
| 453 </data> | |
| 454 <data name="out_strand" format="tabular" label="${tool.name} on ${on_string} problematic SNP report (.strand)"> | |
| 455 <filter>check_mode</filter> | |
| 456 </data> | |
| 457 <data name="out_exclude" format="txt" label="${tool.name} on ${on_string} problematic SNPs to exclude (.exclude)"> | |
| 458 <filter>check_mode</filter> | |
| 459 </data> | |
| 436 <data name="out_log" format="txt" label="${tool.name} on ${on_string} logfile (.log)"/> | 460 <data name="out_log" format="txt" label="${tool.name} on ${on_string} logfile (.log)"/> |
| 437 </outputs> | 461 </outputs> |
| 438 <help><![CDATA[ | 462 <help><![CDATA[ |
| 439 TODO: Fill in help. | 463 TODO: Fill in help. |
| 440 ]]></help> | 464 ]]></help> |