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comparison sampleFasta.xml @ 9:c2c69c6090f0 draft

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author petr-novak
date Fri, 31 Jan 2020 06:55:23 -0500
parents e320ef2d105a
children a675b4534b19
comparison
equal deleted inserted replaced
8:99569eccc583 9:c2c69c6090f0
1 <tool id="sampler" name="Sequence sampling" version="1.0.0"> 1 <tool id="sampler" name="Read sampling" version="1.0.0">
2 <description> Tool for creating samples of sequences from larger dataset</description> 2 <description> Tool for random sampling subsets of reads from larger dataset</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 <command> 9 <command>
10 <![CDATA[
10 #if str($paired)=="true" 11 #if str($paired)=="true"
11 ${__tool_directory__}/deinterlacer.py $input Afile Bfile 12 ${__tool_directory__}/deinterlacer.py $input Afile Bfile
12 &amp;&amp; 13 &&
13 seqkit sample -2 --number $number --rand-seed $seed -o Asample -w 0 Afile 14 seqkit sample -2 --number $number --rand-seed $seed -o Asample -w 0 Afile < /dev/null
14 &amp;&amp; 15 &&
15 seqkit sample -2 --number $number --rand-seed $seed -o Bsample -w 0 Bfile 16 seqkit sample -2 --number $number --rand-seed $seed -o Bsample -w 0 Bfile < /dev/null
16 &amp;&amp; 17 &&
17 ${__tool_directory__}/fasta_interlacer.py -a Asample -b Bsample -p $output -x tmpfile 18 ${__tool_directory__}/fasta_interlacer.py -a Asample -b Bsample -p $output -x tmpfile
18 #else 19 #else
19 seqkit sample -2 --number $number --rand-seed $seed -o $output -w 0 $input 20 seqkit sample -2 --number $number --rand-seed $seed -o $output -w 0 $input
20 #end if 21 #end if
21 </command> 22 ]]>
23 </command>
22 24
23 <inputs> 25 <inputs>
24 <param format="fasta" type="data" name="input" label="Choose your fasta file" /> 26 <param format="fasta" type="data" name="input" label="Read file (FASTA)" />
25 <param name="number" type="integer" size="7" value="500000" min="1" label="number of sequences or sequence pairs"/> 27 <param name="number" type="integer" size="7" value="500000" min="1" label="Number of reads or read pairs"/>
26 <param name="seed" type="integer" size="10" value="10" min="0" label="random number generator seed " /> 28 <param name="seed" type="integer" size="10" value="10" min="0" label="Random number generator seed " />
27 <param name="paired" type="boolean" truevalue="true" falsevalue="false" checked="False" label="All sequence reads are paired" help="check if you are using pair reads and and input sequences contain both read mates and left mates alternate with their right mates"/> 29 <param name="paired" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Paired-end reads" help="If paired-end reads are sampled, left and right-hand reads must be interlaced and all pairs must be complete."/>
28 30
29 31
30 </inputs> 32 </inputs>
31 33
32 34