| Previous changeset 4:5fbeaa41b223 (2017-10-25) Next changeset 6:23f5d9316694 (2017-11-02) |
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Commit message:
correct.py wrapper fix |
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modified:
align_families.xml correct_barcodes.xml dunovo.xml make_families.xml |
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| diff -r 5fbeaa41b223 -r 000969829a5d align_families.xml --- a/align_families.xml Wed Oct 25 19:26:43 2017 -0400 +++ b/align_families.xml Fri Oct 27 12:50:39 2017 -0400 |
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| @@ -6,6 +6,7 @@ <requirement type="package" version="2.0.6">dunovo</requirement> <!-- TODO: require Python 2.7 --> </requirements> + <version_command>align_families.py --version</version_command> <command detect_errors="exit_code">align_families.py --aligner $aligner --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' > '$output' </command> <inputs> |
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| diff -r 5fbeaa41b223 -r 000969829a5d correct_barcodes.xml --- a/correct_barcodes.xml Wed Oct 25 19:26:43 2017 -0400 +++ b/correct_barcodes.xml Fri Oct 27 12:50:39 2017 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.6"> +<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.6.1"> <description>of duplex sequencing reads</description> <requirements> <requirement type="package" version="2.2.5">bowtie2</requirement> @@ -8,12 +8,14 @@ <requirement type="package" version="2.0.6">dunovo</requirement> <!-- TODO: require Python 2.7 --> </requirements> + <version_command>correct.py --version</version_command> <command detect_errors="exit_code"><![CDATA[ - baralign.sh '$input' refdir - | samtools view -S -f 256 - + baralign.sh '$input' refdir correct.sam + && samtools view -S -f 256 correct.sam | correct.py --galaxy $phone --dist $dist --mapq $mapq --pos $pos '$input' refdir/barcodes.fa - | sort - > '$output' + > families.corrected.tsv + && sort families.corrected.tsv + > '$output' ]]> </command> <inputs> |
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| diff -r 5fbeaa41b223 -r 000969829a5d dunovo.xml --- a/dunovo.xml Wed Oct 25 19:26:43 2017 -0400 +++ b/dunovo.xml Fri Oct 27 12:50:39 2017 -0400 |
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| @@ -5,6 +5,7 @@ <requirement type="package" version="2.0.6">dunovo</requirement> <!-- TODO: require Python 2.7 --> </requirements> + <version_command>dunovo.py --version</version_command> <command detect_errors="exit_code"> dunovo.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} --min-reads $min_reads --qual $qual_thres --qual-format $qual_format --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2' #if $keep_sscs: |
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| diff -r 5fbeaa41b223 -r 000969829a5d make_families.xml --- a/make_families.xml Wed Oct 25 19:26:43 2017 -0400 +++ b/make_families.xml Fri Oct 27 12:50:39 2017 -0400 |
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| @@ -5,6 +5,7 @@ <requirement type="package" version="2.0.6">dunovo</requirement> </requirements> <!-- TODO: Add dependency on coreutils to get paste? --> + <version_command>dunovo.py --version</version_command> <command detect_errors="exit_code">make-families.sh -t $taglen -i $invariant '$fastq1' '$fastq2' > '$output' </command> <inputs> |