Mercurial > repos > petr-novak > re_utils
diff sampleFasta.xml @ 22:58807b35777a draft
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
| author | petr-novak |
|---|---|
| date | Wed, 02 Aug 2023 11:31:12 +0000 |
| parents | d14b68e9fd1d |
| children | 628b235d76c7 |
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--- a/sampleFasta.xml Thu Jul 27 09:46:13 2023 +0000 +++ b/sampleFasta.xml Wed Aug 02 11:31:12 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="sampler" name="Read sampling" version="1.0.1"> +<tool id="sampler" name="Read sampling" version="1.0.1.3"> <description> Tool for randomly sampling subsets of reads from large datasets</description> <requirements> <requirement type="package">seqkit</requirement> @@ -6,10 +6,14 @@ <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> + <required_files> + <include type="literal" path="deinterlacer.py" /> + <include type="literal" path="fasta_interlacer.py" /> + </required_files> <command> <![CDATA[ #if str($paired)=="true" - ${__tool_directory__}/deinterlacer.py $input Afile Bfile + python ${__tool_directory__}/deinterlacer.py $input Afile Bfile && NUMBER=\$(($(number) / 2)) && @@ -17,7 +21,7 @@ && seqkit sample -2 --number \$NUMBER --rand-seed $seed -o Bsample -w 0 Bfile < /dev/null && - ${__tool_directory__}/fasta_interlacer.py -a Asample -b Bsample -p $output -x tmpfile + python ${__tool_directory__}/fasta_interlacer.py -a Asample -b Bsample -p $output -x tmpfile #else seqkit sample -2 --number $number --rand-seed $seed -o $output -w 0 $input < /dev/null #end if