Mercurial > repos > thondeboer > neat_genreads
changeset 1:362e0b0f7024 draft
planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
| author | thondeboer |
|---|---|
| date | Tue, 15 May 2018 15:32:13 -0400 |
| parents | 6e75a84e9338 |
| children | 8a739c944dbf |
| files | computeFraglen.xml computeGC.xml genMutModel.xml genSeqErrorModel.xml neat_genreads.xml |
| diffstat | 5 files changed, 8 insertions(+), 3 deletions(-) [+] |
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--- a/computeFraglen.xml Tue May 15 02:39:53 2018 -0400 +++ b/computeFraglen.xml Tue May 15 15:32:13 2018 -0400 @@ -6,6 +6,7 @@ <requirements> <requirement type="package" version="0.1.19">samtools</requirement> <requirement type="package" version="1.9.1">numpy</requirement> + <requirement type="package">libgfortran</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[
--- a/computeGC.xml Tue May 15 02:39:53 2018 -0400 +++ b/computeGC.xml Tue May 15 15:32:13 2018 -0400 @@ -6,12 +6,13 @@ <requirements> <requirement type="package" version="2.25.0">bedtools</requirement> <requirement type="package" version="1.9.1">numpy</requirement> + <requirement type="package">libgfortran</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ bedtools genomecov -d -ibam $bam_file #if $in_type.input_type == "built-in": - -g ${in_type.reference.path} + -g ${in_type.reference.fields.path} #else: -g ${in_type.reference} #end if
--- a/genMutModel.xml Tue May 15 02:39:53 2018 -0400 +++ b/genMutModel.xml Tue May 15 15:32:13 2018 -0400 @@ -6,13 +6,14 @@ <requirements> <requirement type="package" version="1.9.1">numpy</requirement> <requirement type="package">matplotlib</requirement> + <requirement type="package">libgfortran</requirement> </requirements> <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 #if $in_type.input_type == "built-in": - && ln ${in_type.reference.path} reference.fa + && ln ${in_type.reference.fields.path} reference.fa #else: && ln ${in_type.reference} reference.fa #end if
--- a/genSeqErrorModel.xml Tue May 15 02:39:53 2018 -0400 +++ b/genSeqErrorModel.xml Tue May 15 15:32:13 2018 -0400 @@ -6,6 +6,7 @@ <requirements> <requirement type="package" version="1.9.1">numpy</requirement> <requirement type="package">matplotlib</requirement> + <requirement type="package">libgfortran</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[
--- a/neat_genreads.xml Tue May 15 02:39:53 2018 -0400 +++ b/neat_genreads.xml Tue May 15 15:32:13 2018 -0400 @@ -5,12 +5,13 @@ <description>is a fine-grained read simulator</description> <requirements> <requirement type="package" version="1.9.1">numpy</requirement> + <requirement type="package">libgfortran</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ python2 $__tool_directory__/genReads.py #if $in_type.input_type == "built-in": - -r ${in_type.reference.path} + -r ${in_type.reference.fields.path} #else: -r ${in_type.reference} #end if