Mercurial > repos > sanbi-uwc > shapeit_phase
changeset 3:4a048227b86f draft
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 6dfd47f8de029246dd63d60f24ed685a13f8a2ff-dirty
| author | sanbi-uwc |
|---|---|
| date | Fri, 14 Sep 2018 17:09:16 -0400 |
| parents | 4eccc085e9fe |
| children | 39e075021957 |
| files | shapeit_phase.xml |
| diffstat | 1 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/shapeit_phase.xml Fri Sep 14 03:11:54 2018 -0400 +++ b/shapeit_phase.xml Fri Sep 14 17:09:16 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="shapeit_phase" name="shapeit_phase" version="0.2.0"> +<tool id="shapeit_phase" name="shapeit_phase" version="0.3.0"> <description>genomic data with or without reference panel</description> <requirements> @@ -25,7 +25,7 @@ echo "Failed to find valid map file at \${MAP}" >&2 && exit 1 ; fi && - # end + #end if shapeit @@ -48,7 +48,7 @@ #end if #if $use_genetic_map.use_genetic_map_select == "use_genetic_map_yes": - #if $use_genetic_map.genetic_map_from_table == "genetic_map_from_table_yes": + #if $use_genetic_map.genetic_map_from_table_select == "genetic_map_from_table_yes": --input-map \$MAP else: --input-map $use_genetic_map.genetic_map @@ -58,10 +58,10 @@ #end if #if $use_ref_panel.use_ref_panel_select == "use_ref_panel_yes": - #if $use_ref_panel.ref_panel_from_table == "ref_panel_from_table_yes": + #if $use_ref_panel.ref_panel_from_table_select == "ref_panel_from_table_yes": --input-ref \$HAP \$LEGEND \$SAMPLE #else - --input-ref $use_ref_panel.ref_panel_haps $use_ref_panel.ref_panel_legend $use_ref_panel.ref_panel_sample + --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 #end if #if $use_ref_panel.disable_mcmc_iterations == "disable_mcmc_iterations_yes": --no-mcmc @@ -399,8 +399,8 @@ <outputs> <data name="out_haps" format="tabular" label="${tool.name} on ${on_string} haplotypes (.haps)"/> <data name="out_sample" format="tabular" label="${tool.name} on ${on_string} additional information (.sample)"/> - <data name="out_graph" format="text" label="${tool.name} on ${on_string} haplotype graphs (.hgraph)"/> - <data name="out_log" format="text" label="${tool.name} on ${on_string} logfile (.log)"/> + <data name="out_graph" format="txt" label="${tool.name} on ${on_string} haplotype graphs (.hgraph)"/> + <data name="out_log" format="txt" label="${tool.name} on ${on_string} logfile (.log)"/> </outputs> <help><![CDATA[ TODO: Fill in help.