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comparison fermi2.xml @ 4:a206c60df528 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 12:10:15 -0500
parents 3ffa0a5cbd8c
children b7f0625940a4
comparison
equal deleted inserted replaced
3:3ffa0a5cbd8c 4:a206c60df528
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 <(cat 12 -p prefix "
13 #for fastq in $input1: 13 #for fastq in $input1:
14 '$fastq' 14 '$fastq'
15 #end for 15 #end for
16 ) 16 "
17 $T 17 -T $T
18 $2 18 $two_pass_error
19 $E 19 $E
20 > prefix.mak && 20 > prefix.mak &&
21 make -f prefix.mak 21 make -f prefix.mak
22 ]]></command> 22 ]]></command>
23 <inputs> 23 <inputs>
24 <param type="data" multiple="true" name="input1" format="fastqsanger,fastqsanger.gz"/> 24 <param type="data" multiple="true" name="input1" format="fastqsanger,fastqsanger.gz"/>
25 <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"/>
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"/> 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"/>
27 <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"/>
28 <param argument="-2" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/> 28 <param argument="-2" name="two_pass_error" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/>
29 <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"/>
30 </inputs> 30 </inputs>
31 <outputs> 31 <outputs>
32 <data name="unitigs" format="fastqsanger.gz" from_work_dir="prefix.mag.gz"/> 32 <data name="unitigs" format="fastqsanger.gz" from_work_dir="prefix.mag.gz"/>
33 </outputs> 33 </outputs>
34 <tests> 34 <tests>
35 <test> 35 <test>
36 <param name="input1" value="test.fastq.gz"/> 36 <param name="input1" value="test.fastq.gz,test.fastq.gz"/>
37 <param name="readlength" value="150"/> 37 <param name="readlength" value="150"/>
38 <param name="genome_size" value="1"/> 38 <param name="genome_size" value="1"/>
39 <output name="unitigs" file="unitigs.gz" compare="sim_size"/> 39 <output name="unitigs" file="unitigs.gz" compare="sim_size"/>
40 </test> 40 </test>
41 </tests> 41 </tests>