Mercurial > repos > sanbi-uwc > shapeit_phase
changeset 13:b69dadabf671 draft
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
| author | sanbi-uwc |
|---|---|
| date | Tue, 18 Sep 2018 06:28:10 -0400 |
| parents | 557cc7904a2b |
| children | f92f1cc9e382 |
| files | shapeit_phase.xml |
| diffstat | 1 files changed, 14 insertions(+), 7 deletions(-) [+] |
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--- a/shapeit_phase.xml Tue Sep 18 06:12:53 2018 -0400 +++ b/shapeit_phase.xml Tue Sep 18 06:28:10 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="shapeit_phase" name="shapeit_phase" version="0.11.0"> +<tool id="shapeit_phase" name="shapeit_phase" version="0.12.0"> <description>genomic data with or without reference panel</description> <requirements> @@ -9,7 +9,7 @@ </stdio> <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($input_files.input_type_select) == 'plink_bed_bim_fam_list': + #if str($input_files.input_type_select) == 'plink_bed_bim_fam_list': 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 '${input_files.plink_bed_etc_list[2]}' input.plink_fam && @@ -21,9 +21,13 @@ head -2 input.plink_fam && PART=`head -1 input.plink_bim | cut -f1` && echo "Working on PART: \$PART" && - REF_DIR='${use_genetic_map.genetic_map_from_table.map_from_table.fields.path}' && - REF_PREFIX='${use_genetic_map.genetic_map_from_table.map_from_table.fields.reference_prefix}' && - SAMPLE_PREFIX="\$REF_DIR/${use_genetic_map.genetic_map_from_table.map_from_table.fields.sample_prefix}" && + #else + PART='' + #end if + #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": + REF_DIR='${use_ref_panel.ref_panel_from_table.ref_from_table.fields.path}' && + REF_PREFIX='${use_ref_panel.ref_panel_from_table.ref_from_table.fields.reference_prefix}' && + SAMPLE_PREFIX="\$REF_DIR/${use_ref_panel.ref_panel_from_table.ref_from_table.fields.sample_prefix}" && SAMPLE=`ls \$SAMPLE_PREFIX*.sample` && if [ ! -f "\$SAMPLE" ] ; then echo "Failed to find valid sample file at \$SAMPLE" >&2 && @@ -39,8 +43,11 @@ echo "Failed to find valid .legend file at \$LEGEND" >&2 && exit 1 ; fi && + #end if + #if $use_genetic_map.genetic_map_select == "use_genetic_map_yes" && $use_genetic_map.genetic_map_from_table.genetic_map_from_table_select == "genetic_map_from_table_yes": + MAP_DIR='${use_genetic_map.genetic_map_from_table.map_from_table.fields.path}' && MAP_PREFIX='${use_genetic_map.genetic_map_from_table.map_from_table.fields.map_prefix}' && - MAP=`ls \${REF_DIR}/\${MAP_PREFIX}\${PART}_*` && + MAP=`ls \${MAP_DIR}/\${MAP_PREFIX}\${PART}_*` && if [ ! -f "\${MAP}" ] ; then echo "Failed to find valid map file at \${MAP}" >&2 && exit 1 ; @@ -49,7 +56,7 @@ #if $input_files.input_type_select == "plink_bed_bim_fam_list": echo "COLLECTION NAME:" ${input_files.plink_bed_etc_list.name} && #for $dat in $input_files.plink_bed_etc_list: - echo NAME '${dat.name}' && + echo Processing NAME '${dat.name}' && #end for #end if