Mercurial > repos > iuc > bedtools

comparison maskFastaBed.xml @ 33:87ee588b3d45 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0a8cabcc8f00014789b6d30e90be1b949d4e94d2
author iuc
date Mon, 17 Dec 2018 14:23:31 -0500
parents 4f7a5ccd2ae9
children dde39ba9c031
comparison
equal deleted inserted replaced
32:4f7a5ccd2ae9 33:87ee588b3d45
23 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"
24 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)" />
25 <param name="mc" type="text" value="N" 25 <param name="mc" type="text" value="N"
26 label="Replace masking character" 26 label="Replace masking character"
27 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="" 28 <param argument="-fullHeader" name="fullheader" type="boolean" truevalue="-fullHeader" falsevalue=""
29 label="Use full fasta header." 29 label="Use full fasta header."
30 help="By default, only the word before the first space or tab is used"/> 30 help="By default, only the word before the first space or tab is used"/>
31 </inputs> 31 </inputs>
32 <outputs> 32 <outputs>
33 <data format="fasta" name="output" /> 33 <data format="fasta" name="output" />
35 <tests> 35 <tests>
36 <test> 36 <test>
37 <param name="input" value="nucBed1.bed" ftype="bed" /> 37 <param name="input" value="nucBed1.bed" ftype="bed" />
38 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> 38 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
39 <param name="soft" value="False" /> 39 <param name="soft" value="False" />
40 <output name="output" file="maskFastaBed_result1.bed" ftype="fasta" /> 40 <output name="output" file="maskFastaBed_result1.fasta" ftype="fasta" />
41 </test> 41 </test>
42 <test> 42 <test>
43 <param name="input" value="nucBed1.bed" ftype="bed" /> 43 <param name="input" value="nucBed1.bed" ftype="bed" />
44 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> 44 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
45 <param name="soft" value="True" /> 45 <param name="soft" value="True" />
46 <output name="output" file="maskFastaBed_result2.bed" ftype="fasta" /> 46 <output name="output" file="maskFastaBed_result2.fasta" ftype="fasta" />
47 </test>
48 <test>
49 <param name="input" value="nucBed1.bed" ftype="bed" />
50 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
51 <param name="soft" value="True" />
52 <param name="fullheader" value="True" />
53 <output name="output" file="maskFastaBed_result3.fasta" ftype="fasta" />
47 </test> 54 </test>
48 </tests> 55 </tests>
49 <help> 56 <help>
50 <![CDATA[ 57 <![CDATA[
51 **What it does** 58 **What it does**