| Previous changeset 2:7f59ee641f70 (2017-03-13) |
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Commit message:
planemo upload commit cf7305a207096e24bedddb0cb55bed86a6b7cd6b |
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modified:
kat_sect.xml |
| b |
| diff -r 7f59ee641f70 -r 624f99fe1705 kat_sect.xml --- a/kat_sect.xml Mon Mar 13 15:53:39 2017 -0400 +++ b/kat_sect.xml Wed Mar 15 13:56:48 2017 -0400 |
| b |
| @@ -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@ |