Mercurial > repos > sanbi-uwc > shapeit_phase
changeset 17:1f460ad509b6 draft
planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
| author | sanbi-uwc |
|---|---|
| date | Tue, 18 Sep 2018 08:55:42 -0400 |
| parents | 1a00583b6b2c |
| children | d3515c2a3f51 |
| files | shapeit_phase.xml |
| diffstat | 1 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/shapeit_phase.xml Tue Sep 18 08:48:52 2018 -0400 +++ b/shapeit_phase.xml Tue Sep 18 08:55:42 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="shapeit_phase" name="shapeit_phase" version="0.15.0"> +<tool id="shapeit_phase" name="shapeit_phase" version="0.16.0"> <description>genomic data with or without reference panel</description> <requirements> <requirement type="package" version="2.r837">shapeit</requirement> @@ -7,7 +7,7 @@ <exit_code range="1:" /> </stdio> - <command><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ #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 && @@ -182,12 +182,13 @@ --output-log $out_log #else --output-log output - && mv output.mendel.log $out_log + | grep -v 'ERROR: Reference and Main panels are not well aligned:' + ; mv output.mendel.log $out_log && mv output.mendel.snp.strand $out_strand && mv output.mendel.snp.strand.exclude $out_exclude #end if + # NOTE that in check mode we are ignoring the error related to panel misalignment ]]></command> - <inputs> <param name="check_mode" type="boolean" truevalue="-check" falsevalue="" label="Run in -check mode (check data)" /> <conditional name="input_files">