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comparison maskFastaBed.xml @ 19:a8eabd2838f6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
author iuc
date Fri, 08 Dec 2017 03:26:42 -0500
parents c78cf6fe3018
children 95a3b2c25bd1
comparison
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18:18aeac3cd1db 19:a8eabd2838f6
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 bedtools maskfasta 10 bedtools maskfasta
11 $soft 11 $soft
12 -mc "${mc}" 12 -mc '${mc}'
13 -fi "${fasta}" 13 -fi '${fasta}'
14 -bed "${input}" 14 -bed '${input}'
15 -fo "${output}" 15 -fo '${output}'
16 $fullheader
16 ]]> 17 ]]>
17 </command> 18 </command>
18 <inputs> 19 <inputs>
19 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/> 20 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
20 <param format="fasta" name="fasta" type="data" label="Fasta file"/> 21 <param format="fasta" name="fasta" type="data" label="Fasta file"/>
22 label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence" 23 label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence"
23 help="By default, hard-masking (that is, conversion to Ns) is performed. (-soft)" /> 24 help="By default, hard-masking (that is, conversion to Ns) is performed. (-soft)" />
24 <param name="mc" type="text" value="N" 25 <param name="mc" type="text" value="N"
25 label="Replace masking character" 26 label="Replace masking character"
26 help="That is, instead of masking with Ns, use another character. (-mc)" /> 27 help="That is, instead of masking with Ns, use another character. (-mc)" />
28 <param argument="-fullheader" type="boolean" truevalue="-fullheader" falsevalue=""
29 label="Use full fasta header."
30 help="By default, only the word before the first space or tab is used"/>
27 </inputs> 31 </inputs>
28 <outputs> 32 <outputs>
29 <data format="fasta" name="output" /> 33 <data format="fasta" name="output" />
30 </outputs> 34 </outputs>
31 <tests> 35 <tests>