Mercurial > repos > iuc > gatk4_mutect2
changeset 2:3be27a9a7313 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 093a027ca9e7d34e7d12cd14ca0d0dacadfcb78b"
| author | iuc |
|---|---|
| date | Fri, 10 Apr 2020 14:10:55 -0400 |
| parents | fd2d6e035c3f |
| children | 287c4af133e6 |
| files | gatk4_Mutect2.xml macros.xml |
| diffstat | 2 files changed, 5 insertions(+), 8 deletions(-) [+] |
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--- a/gatk4_Mutect2.xml Mon Nov 18 13:45:47 2019 -0500 +++ b/gatk4_Mutect2.xml Fri Apr 10 14:10:55 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@1" profile="18.05"> +<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@2" profile="18.05"> <description>- Call somatic SNVs and indels via local assembly of haplotypes</description> <macros> <import>macros.xml</import> @@ -38,8 +38,8 @@ #end if #end if - @CMD_BEGIN@ GetSampleName --input="input.bam" --output="samplename.txt" && - sample=`cat samplename.txt` && + gatk GetSampleName --input="input.bam" --output="samplename.txt" && + sample=`cat samplename.txt | sed 's/"//g'` && #if str($optional.optional_parameters) == 'yes' #if $optional.panel_of_normals @@ -76,7 +76,7 @@ #end if - @CMD_BEGIN@ Mutect2 --QUIET $ref_flag --tumor-sample \$sample + gatk Mutect2 --QUIET $ref_flag --tumor-sample "\$sample" #include source=$gatk_bam_input# @@ -770,4 +770,4 @@ <citations> <expand macro="citations"/> </citations> -</tool> \ No newline at end of file +</tool>
--- a/macros.xml Mon Nov 18 13:45:47 2019 -0500 +++ b/macros.xml Fri Apr 10 14:10:55 2020 -0400 @@ -17,9 +17,6 @@ <version_command>gatk SortSam --version 2>&1 | grep Version | cut -d ':' -f 2</version_command> </xml> - <!--Command token, java options should not be hard coded here.--> - <token name="@CMD_BEGIN@">[[ -z \$_JAVA_OPTIONS ]] && export JAVA_OPTS=\$_JAVA_OPTIONS && gatk</token> - <!--Define sections that parameters could exist within.--> <template name="set_sections"> #set global $sections = ['', 'optional.', 'advanced.', 'deprecated.']