Mercurial > repos > morinlab > vcf2maf
comparison vcf2maf.xml @ 10:fa20a5e56cf2 draft default tip
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| author | morinlab |
|---|---|
| date | Fri, 27 Jan 2017 20:25:23 -0500 |
| parents | 4e76e1a1790e |
| children |
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| 9:4e76e1a1790e | 10:fa20a5e56cf2 |
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| 21 --vep-path \$ENSEMBL_VEP_84_INSTALL_DIR | 21 --vep-path \$ENSEMBL_VEP_84_INSTALL_DIR |
| 22 --vep-data \${ENSEMBL_VEP_84_INSTALL_DIR}/cache | 22 --vep-data \${ENSEMBL_VEP_84_INSTALL_DIR}/cache |
| 23 --ref-fasta \${ENSEMBL_VEP_84_INSTALL_DIR}/cache/`echo $species_select.value | sed 's/-/\t/g' | cut -f1`/84_`echo $species_select.value | sed 's/-/\t/g' | cut -f2`/*.fa | 23 --ref-fasta \${ENSEMBL_VEP_84_INSTALL_DIR}/cache/`echo $species_select.value | sed 's/-/\t/g' | cut -f1`/84_`echo $species_select.value | sed 's/-/\t/g' | cut -f2`/*.fa |
| 24 --species `echo $species_select.value | sed 's/-/\t/g' | cut -f1` | 24 --species `echo $species_select.value | sed 's/-/\t/g' | cut -f1` |
| 25 --ncbi-build `echo $species_select.value | sed 's/-/\t/g' | cut -f2`; | 25 --ncbi-build `echo $species_select.value | sed 's/-/\t/g' | cut -f2`; |
| 26 mv $output_maf temp.maf; | |
| 27 grep -v version temp.maf > $output_maf; | |
| 26 </command> | 28 </command> |
| 27 | 29 |
| 28 <inputs> | 30 <inputs> |
| 29 <conditional name="sampleid_source"> | 31 <conditional name="sampleid_source"> |
| 30 <param label="Choose the source to open the Sample Id" name="sampleid_selector" type="select"> | 32 <param label="Choose the source to open the Sample Id" name="sampleid_selector" type="select"> |