Mercurial > repos > sanbi-uwc > shapeit_phase
changeset 9:9f7a81693561 draft
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
| author | sanbi-uwc |
|---|---|
| date | Tue, 18 Sep 2018 01:49:22 -0400 |
| parents | 00788810fe57 |
| children | 03af7e3e3b2f |
| files | shapeit_phase.xml |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/shapeit_phase.xml Tue Sep 18 01:25:46 2018 -0400 +++ b/shapeit_phase.xml Tue Sep 18 01:49:22 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="shapeit_phase" name="shapeit_phase" version="0.7.0"> +<tool id="shapeit_phase" name="shapeit_phase" version="0.8.0"> <description>genomic data with or without reference panel</description> <requirements> @@ -11,7 +11,7 @@ <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` && - echo "Working on PART: $PART" && + echo "Working on PART: \$PART" && REF_DIR='${use_genetic_map.genetic_map_from_table.map_from_table.fields.path}' && REF_PREFIX='${use_genetic_map.genetic_map_from_table.map_from_table.fields.reference_prefix}' && SAMPLE_PREFIX="\$REF_DIR/${use_genetic_map.genetic_map_from_table.map_from_table.fields.sample_prefix}" &&