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comparison fermi2.xml @ 2:adf010a51dde draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
author mvdbeek
date Fri, 30 Dec 2016 11:47:07 -0500
parents b808c0bc19a9
children 3ffa0a5cbd8c
comparison
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1:c6b11ead6f1f 2:adf010a51dde
7 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 fermi2.pl unitig 8 fermi2.pl unitig
9 -s$genome_size 9 -s$genome_size
10 -t\${GALAXY_SLOTS:-4} 10 -t\${GALAXY_SLOTS:-4}
11 -l$readlength 11 -l$readlength
12 -p prefix '$input1' 12 -p prefix <(cat
13 #for fastq in '$input1':
14 '$fastq'
15 #end for
16 )
13 $T 17 $T
14 $2 18 $2
15 $E 19 $E
16 > prefix.mak && 20 > prefix.mak &&
17 make -f prefix.mak 21 make -f prefix.mak
18 ]]></command> 22 ]]></command>
19 <inputs> 23 <inputs>
20 <param type="data" name="input1" format="fastqsanger,fastqsanger.gz"/> 24 <param type="data" multiple="true" name="input1" format="fastqsanger,fastqsanger.gz"/>
21 <param argument="-l" name="readlength" type="integer" label="primary read length" value="101" min="70"/> 25 <param argument="-l" name="readlength" type="integer" label="primary read length" value="101" min="70"/>
22 <param argument="-s" name="genome_size" type="integer" value="180000" min="1" label="approximate genome size in kilobases" help="Enter approximate genome size in kilobases. For a human genome of 3.2 gigabases enter 3200000"/> 26 <param argument="-s" name="genome_size" type="integer" value="180000" min="1" label="approximate genome size in kilobases" help="Enter approximate genome size in kilobases. For a human genome of 3.2 gigabases enter 3200000"/>
23 <param argument="-T" type="integer" value="61" label="use INT-mer for post-trimming/filtering" min="10"/> 27 <param argument="-T" type="integer" value="61" label="use INT-mer for post-trimming/filtering" min="10"/>
24 <param argument="-2" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/> 28 <param argument="-2" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/>
25 <param argument="-E" type="boolean" checked="false" truevalue="-E" falsevalue="" label="Do not apply error correction"/> 29 <param argument="-E" type="boolean" checked="false" truevalue="-E" falsevalue="" label="Do not apply error correction"/>