Mercurial > repos > sanbi-uwc > shapeit_phase
changeset 11:f25ff17454f4 draft
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
| author | sanbi-uwc |
|---|---|
| date | Tue, 18 Sep 2018 05:50:58 -0400 |
| parents | 03af7e3e3b2f |
| children | 557cc7904a2b |
| files | shapeit_phase.xml |
| diffstat | 1 files changed, 11 insertions(+), 11 deletions(-) [+] |
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--- a/shapeit_phase.xml Tue Sep 18 01:54:33 2018 -0400 +++ b/shapeit_phase.xml Tue Sep 18 05:50:58 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="shapeit_phase" name="shapeit_phase" version="0.9.0"> +<tool id="shapeit_phase" name="shapeit_phase" version="0.10.0"> <description>genomic data with or without reference panel</description> <requirements> @@ -10,7 +10,16 @@ <command><![CDATA[ #if str($use_ref_panel.use_ref_panel_select) == "use_ref_panel_yes" and str($use_ref_panel.ref_panel_from_table.ref_panel_from_table_select) == "ref_panel_from_table_yes" and str($input_files.input_type_select) == 'plink_bed_bim_fam_list': - PART=`head -1 myfile.bim | cut -f1` && + ln -s '${input_files.plink_bed_etc_list[0]}' input.plink_bed && + ln -s '${input_files.plink_bed_etc_list[1]}' input.plink_bim && + ln -s '${input_files.plink_bed_etc_list[2]}' input.plink_fam && + echo "BED file" && + ls -l input.plink_bed && + echo "BIM file" && + head -2 input.plink_bim && + echo "FAM file" && + head -2 input.plink_fam && + PART=`head -1 input.plink_bim | cut -f1` && echo "Working on PART: \$PART" && REF_DIR='${use_genetic_map.genetic_map_from_table.map_from_table.fields.path}' && REF_PREFIX='${use_genetic_map.genetic_map_from_table.map_from_table.fields.reference_prefix}' && @@ -42,15 +51,6 @@ #for $dat in $input_files.plink_bed_etc_list: echo NAME '${dat.name}' && #end for - ln -s '${input_files.plink_bed_etc_list[0]}' input.plink_bed && - ln -s '${input_files.plink_bed_etc_list[1]}' input.plink_bim && - ln -s '${input_files.plink_bed_etc_list[2]}' input.plink_fam && - echo "BED file" && - ls -l input.plink_bed && - echo "BIM file" && - head -2 input.plink_bim && - echo "FAM file" && - head -2 input.plink_fam && #end if shapeit