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comparison sampleFasta.xml @ 22:58807b35777a draft

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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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21:f4ed6a65a2ff 22:58807b35777a
1 <tool id="sampler" name="Read sampling" version="1.0.1"> 1 <tool id="sampler" name="Read sampling" version="1.0.1.3">
2 <description> Tool for randomly sampling subsets of reads from large datasets</description> 2 <description> Tool for randomly sampling subsets of reads from large datasets</description>
3 <requirements> 3 <requirements>
4 <requirement type="package">seqkit</requirement> 4 <requirement type="package">seqkit</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" level="fatal" description="Error" /> 7 <exit_code range="1:" level="fatal" description="Error" />
8 </stdio> 8 </stdio>
9 <required_files>
10 <include type="literal" path="deinterlacer.py" />
11 <include type="literal" path="fasta_interlacer.py" />
12 </required_files>
9 <command> 13 <command>
10 <![CDATA[ 14 <![CDATA[
11 #if str($paired)=="true" 15 #if str($paired)=="true"
12 ${__tool_directory__}/deinterlacer.py $input Afile Bfile 16 python ${__tool_directory__}/deinterlacer.py $input Afile Bfile
13 && 17 &&
14 NUMBER=\$(($(number) / 2)) 18 NUMBER=\$(($(number) / 2))
15 && 19 &&
16 seqkit sample -2 --number \$NUMBER --rand-seed $seed -o Asample -w 0 Afile < /dev/null 20 seqkit sample -2 --number \$NUMBER --rand-seed $seed -o Asample -w 0 Afile < /dev/null
17 && 21 &&
18 seqkit sample -2 --number \$NUMBER --rand-seed $seed -o Bsample -w 0 Bfile < /dev/null 22 seqkit sample -2 --number \$NUMBER --rand-seed $seed -o Bsample -w 0 Bfile < /dev/null
19 && 23 &&
20 ${__tool_directory__}/fasta_interlacer.py -a Asample -b Bsample -p $output -x tmpfile 24 python ${__tool_directory__}/fasta_interlacer.py -a Asample -b Bsample -p $output -x tmpfile
21 #else 25 #else
22 seqkit sample -2 --number $number --rand-seed $seed -o $output -w 0 $input < /dev/null 26 seqkit sample -2 --number $number --rand-seed $seed -o $output -w 0 $input < /dev/null
23 #end if 27 #end if
24 ]]> 28 ]]>
25 </command> 29 </command>