Mercurial > repos > nml > kat_sect
changeset 3:624f99fe1705 draft default tip
planemo upload commit cf7305a207096e24bedddb0cb55bed86a6b7cd6b
| author | nml |
|---|---|
| date | Wed, 15 Mar 2017 13:56:48 -0400 |
| parents | 7f59ee641f70 |
| children | |
| files | kat_sect.xml |
| diffstat | 1 files changed, 7 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/kat_sect.xml Mon Mar 13 15:53:39 2017 -0400 +++ b/kat_sect.xml Wed Mar 15 13:56:48 2017 -0400 @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.1"> +<tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.2"> <description> Estimates the coverage of each sequence in a file using K-mers from another sequence file(s).</description> <macros> <token name="@EXECUTABLE@">sect</token> @@ -12,17 +12,17 @@ cp "$db" db.fasta && #if $single_or_paired.type == "single" - ln "$input_se" "$single_or_paired.input_se.element_identifier".fastq && + ln "$input_se" read.fastq && kat sect 'db.fasta' - "$single_or_paired.input_se.element_identifier".fastq + read.fastq #elif $single_or_paired.type == "paired" - ln "$single_or_paired.forward_pe" "$single_or_paired.forward_pe.name"_1.fastq && ln "$single_or_paired.reverse_pe" "$single_or_paired.forward_pe.name"_2.fastq && + ln "$single_or_paired.forward_pe" read_1.fastq && ln "$single_or_paired.reverse_pe" read_2.fastq && kat sect 'db.fasta' - "$single_or_paired.forward_pe.name"_1.fastq "$single_or_paired.forward_pe.name"_2.fastq + read_1.fastq read_2.fastq #else - ln "$single_or_paired.fastq_collection.forward" "$single_or_paired.fastq_collection.forward.name"_1.fastq && ln "$single_or_paired.fastq_collection.reverse" "$single_or_paired.fastq_collection.forward.name"_2.fastq && + ln "$single_or_paired.fastq_collection.forward" read_1.fastq && ln "$single_or_paired.fastq_collection.reverse" read_2.fastq && kat sect 'db.fasta' - "$single_or_paired.fastq_collection.forward.name"_1.fastq "$single_or_paired.fastq_collection.forward.name"_2.fastq + read_1.fastq read_2.fastq #end if @THREADS@