Mercurial > repos > thondeboer > neat_genreads
changeset 9:441103f02a11 draft
planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
| author | thondeboer |
|---|---|
| date | Wed, 16 May 2018 02:05:26 -0400 |
| parents | dc383ecbf839 |
| children | 7d10b55965c9 |
| files | computeGC.xml genMutModel.xml genSeqErrorModel.xml |
| diffstat | 3 files changed, 11 insertions(+), 11 deletions(-) [+] |
line wrap: on
line diff
--- a/computeGC.xml Tue May 15 23:09:17 2018 -0400 +++ b/computeGC.xml Wed May 16 02:05:26 2018 -0400 @@ -15,8 +15,8 @@ #else: -g ${in_type.reference} #end if - > out.genomecov - && python2 $__tool_directory__/utilities/computeGC.py + > out.genomecov; + python2 $__tool_directory__/utilities/computeGC.py #if $in_type.input_type == "built-in": -r ${in_type.reference.fields.path} #else:
--- a/genMutModel.xml Tue May 15 23:09:17 2018 -0400 +++ b/genMutModel.xml Wed May 16 02:05:26 2018 -0400 @@ -10,13 +10,13 @@ <command detect_errors="exit_code"> <![CDATA[ ## Filenames and extensions are important, so make some links to make life easier downstream - ln -s $mutation_file mutation_file.vcf + ln -s $mutation_file mutation_file.vcf; #if $in_type.input_type == "built-in": - && ln -s ${in_type.reference.fields.path} reference.fa + ln -s ${in_type.reference.fields.path} reference.fa; #else: - && ln -s ${in_type.reference} reference.fa + ln -s ${in_type.reference} reference.fa; #end if - && python2 $__tool_directory__/utilities/genMutModel.py + python2 $__tool_directory__/utilities/genMutModel.py -r reference.fa -m mutation_file.vcf -o $genMutModel_modelfile
--- a/genSeqErrorModel.xml Tue May 15 23:09:17 2018 -0400 +++ b/genSeqErrorModel.xml Wed May 16 02:05:26 2018 -0400 @@ -10,21 +10,21 @@ <command detect_errors="exit_code"> <![CDATA[ #if $lib_type_cond.read1.ext == "fastqsanger.gz": - ln -s $lib_type_cond.read1 read1.fq.gz + ln -s $lib_type_cond.read1 read1.fq.gz; #set $read1="read1.fq.gz" #if $lib_type_cond.lib_type == 'paired': - && ln -s $lib_type_cond.read2 read2.fq.gz + ln -s $lib_type_cond.read2 read2.fq.gz; #set $read2="read2.fq.gz" #end if #else - ln -s $lib_type_cond.read1 read1.fq + ln -s $lib_type_cond.read1 read1.fq; #set $read1="read1.fq" #if $lib_type_cond.lib_type == 'paired': - && ln -s $lib_type_cond.read2 read2.fq + ln -s $lib_type_cond.read2 read2.fq; #set $read2="read2.fq" #end if #end if - && python2 $__tool_directory__/utilities/genSeqErrorModel.py + python2 $__tool_directory__/utilities/genSeqErrorModel.py -i $read1 #if $lib_type_cond.lib_type == 'paired': -i2 $read2