Mercurial > repos > sanbi-uwc > shapeit_phase
changeset 5:ceb05c9e6d0a draft
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
| author | sanbi-uwc |
|---|---|
| date | Mon, 17 Sep 2018 06:06:18 -0400 |
| parents | 39e075021957 |
| children | 9edc0fb317f7 |
| files | shapeit_phase.xml tool-data/shapeit_ref.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 44 insertions(+), 18 deletions(-) [+] |
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--- a/shapeit_phase.xml Fri Sep 14 17:18:14 2018 -0400 +++ b/shapeit_phase.xml Mon Sep 17 06:06:18 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="shapeit_phase" name="shapeit_phase" version="0.4.0"> +<tool id="shapeit_phase" name="shapeit_phase" version="0.5.0"> <description>genomic data with or without reference panel</description> <requirements> @@ -9,23 +9,49 @@ </stdio> <command><![CDATA[ - #if str($use_ref_panel) == "use_ref_panel_yes" and str($use_ref_panel.ref_panel_from_table) == "ref_panel_from_table_yes" and str($input_files.input_type_select) == 'plink_bed_bim_fam_list': - # this is all expecting 1000GP-style reference data + #if str($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` && - REF_DIR='${use_genetic_map.map_from_table.fields.path}' && - REF_PREFIX='${use_genetic_map.map_from_table.fields.reference_prefix}' && - if [ -f "\${REF_DIR}/\${REF_PREFIX}_\${PART}.hap.gz" ] \; then - HAP="\${REF_DIR}/\${REF_PREFIX}_\${PART}.hap.gz" && - LEGEND="\${REF_DIR}/\${REF_PREFIX}_\${PART}.legend.gz" && - SAMPLE="\${REF_DIR}/\${REF_PREFIX}.sample" ; + 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}" && + SAMPLE=`ls \$SAMPLE_PREFIX*.sample` && + if [ ! -f "\$SAMPLE" ] ; then + echo "Failed to find valid sample file at \$SAMPLE" >&2 && + exit 1 ; fi && - MAP_PREFIX='${use_genetic_map.map_from_table.fields.map_prefix}' && - MAP=`ls \${REF_DIR}/\${MAP_PREFIX}_\${PART}_*` && + HAP="\${REF_DIR}/\${REF_PREFIX}\${PART}.hap.gz" && + if [ -f "\$HAP" ] ; then + echo "Failed to find valid .hap file at \$HAP" >&2 && + exit 1 ; + fi && + LEGEND="\${REF_DIR}/\${REF_PREFIX}\${PART}.legend.gz" && + if [ -f "\$LEGEND ] ; then + echo "Failed to find valid .legend file at \$LEGEND" >&2 && + exit 1 ; + fi && + MAP_PREFIX='${use_genetic_map.genetic_map_from_table.map_from_table.fields.map_prefix}' && + MAP=`ls \${REF_DIR}/\${MAP_PREFIX}\${PART}_*` && if [ ! -f "\${MAP}" ] ; then echo "Failed to find valid map file at \${MAP}" >&2 && exit 1 ; fi && #end if + #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}' && + #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 @@ -39,7 +65,7 @@ #else if $input_files.input_type_select == "plink_bed_bim_fam": --input-bed ${input_files.plink_bed} ${input_files.plink_bim} ${input_files.plink_fam} #else if $input_files.input_type_select == "plink_bed_bim_fam_list": - --input-bed '${input_files.plink_bed_etc_list}[0]' '${input_files.plink_bed_etc_list}[1]' '${input_files.plink_bed_etc_list}[2]' + --input-bed input.plink_bed input.plink_bim input.plink_fam #else if $input_files.inputy_type_select == "oxford_gen_sample": --input-gen ${input_files.oxford_gen} ${input_files.oxford_sample} #if $input_files.oxford_threshold != "0.9": @@ -48,9 +74,9 @@ #end if #if $use_genetic_map.use_genetic_map_select == "use_genetic_map_yes": - #if $use_genetic_map.genetic_map_from_table_select == "genetic_map_from_table_yes": + #if $use_genetic_map.genetic_map_from_table.genetic_map_from_table_select == "genetic_map_from_table_yes": --input-map \$MAP - else: + #else: --input-map $use_genetic_map.genetic_map #end if #else if $use_genetic_map.rho != "0.0004": @@ -58,7 +84,7 @@ #end if #if $use_ref_panel.use_ref_panel_select == "use_ref_panel_yes": - #if $use_ref_panel.ref_panel_from_table_select == "ref_panel_from_table_yes": + #if $use_ref_panel.ref_panel_from_table.ref_panel_from_table_select == "ref_panel_from_table_yes": --input-ref \$HAP \$LEGEND \$SAMPLE #else --input-ref $use_ref_panel.ref_panel_from_table.ref_panel_haps $use_ref_panel.ref_panel_from_table.ref_panel_legend $use_ref_panel.ref_panel_from_table.ref_panel_sample
--- a/tool-data/shapeit_ref.loc.sample Fri Sep 14 17:18:14 2018 -0400 +++ b/tool-data/shapeit_ref.loc.sample Mon Sep 17 06:06:18 2018 -0400 @@ -1,7 +1,7 @@ #This file lists the locations of SHAPEIT reference data connections # -#<value> <description> <path> <reference_file_prefix> <map_file_prefix> +#<value> <description> <path> <reference_file_prefix> <map_file_prefix> <sample_file_prefix> # #For example # -#1000G_Phase3 1000 Genomes project haplotypes /path/to/shapeit_ref/1000G 1000GP_Phase3_ genetic_map_ +#1000G_Phase3 1000 Genomes project haplotypes /path/to/shapeit_ref/1000G 1000GP_Phase3_chr genetic_map_chr 1000GP_Phase3
--- a/tool_data_table_conf.xml.sample Fri Sep 14 17:18:14 2018 -0400 +++ b/tool_data_table_conf.xml.sample Mon Sep 17 06:06:18 2018 -0400 @@ -1,6 +1,6 @@ <tables> <table name="shapeit_ref" comment_char="#"> - <columns>value, name, path, reference_prefix, map_prefix</columns> + <columns>value, name, path, reference_prefix, map_prefix, sample_prefix</columns> <file path="tool-data/shapeit_ref.loc" /> </table> </tables> \ No newline at end of file