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soft link files and remove trailing whitespace #279

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0a3ad79
soft link files and remove trailing whitespace
Takadonet Mar 20, 2026
203a92c
add new version
Takadonet Mar 20, 2026
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22 changes: 11 additions & 11 deletions tools/kat_sect/kat_sect.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version='1.0' encoding='utf-8'?>
<tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.2">
<tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.2+galaxy1">
<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>
Expand All @@ -12,28 +12,28 @@

cp "$db" db.fasta &&
#if $single_or_paired.type == "single"
ln "$input_se" read.fastq &&
ln -s "$input_se" read.fastq &&
kat sect 'db.fasta'
read.fastq
#elif $single_or_paired.type == "paired"
ln "$single_or_paired.forward_pe" read_1.fastq && ln "$single_or_paired.reverse_pe" read_2.fastq &&
ln -s "$single_or_paired.forward_pe" read_1.fastq && ln -s "$single_or_paired.reverse_pe" read_2.fastq &&
kat sect 'db.fasta'
read_1.fastq read_2.fastq
#else
ln "$single_or_paired.fastq_collection.forward" read_1.fastq && ln "$single_or_paired.fastq_collection.reverse" read_2.fastq &&
ln -s "$single_or_paired.fastq_collection.forward" read_1.fastq && ln -s "$single_or_paired.fastq_collection.reverse" read_2.fastq &&
kat sect 'db.fasta'
read_1.fastq read_2.fastq
#end if
#end if

@THREADS@

--mer_len $kmer


$keep_counts

-o results

]]></command>
<inputs>
<expand macro="macro_input" />
Expand Down Expand Up @@ -61,12 +61,12 @@
<param name="keep_counts" value="True" />
<output file="kat-sect-stats.tsv" name="stats" />
<output file="kat-sect-counts.cvg" name="counts" />
</test>
</test>
</tests>
<help><![CDATA[
https://kat.readthedocs.io/en/latest/using.html#sect
]]>

</help>
<expand macro="citations" />
</tool>
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