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comparison maskFastaBed.xml @ 34:dde39ba9c031 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:55:48 -0400
parents 87ee588b3d45
children 3e38c9b3214f
comparison
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_maskfastabed" name="bedtools MaskFastaBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_maskfastabed" name="bedtools MaskFastaBed" version="@TOOL_VERSION@">
2 <description>use intervals to mask sequences from a FASTA file</description> 2 <description>use intervals to mask sequences from a FASTA file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command><![CDATA[
9 <![CDATA[ 9 bedtools maskfasta
10 bedtools maskfasta 10 $soft
11 $soft 11 -mc '${mc}'
12 -mc '${mc}' 12 -fi '${fasta}'
13 -fi '${fasta}' 13 -bed '${input}'
14 -bed '${input}' 14 -fo '${output}'
15 -fo '${output}' 15 $fullheader
16 $fullheader 16 ]]></command>
17 ]]>
18 </command>
19 <inputs> 17 <inputs>
20 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 18 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
21 <param format="fasta" name="fasta" type="data" label="Fasta file"/> 19 <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file"/>
22 <param name="soft" type="boolean" checked="false" truevalue="-soft" falsevalue="" 20 <param argument="-soft" type="boolean" truevalue="-soft" falsevalue="" checked="false"
23 label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence" 21 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)" /> 22 help="By default, hard-masking (that is, conversion to Ns) is performed" />
25 <param name="mc" type="text" value="N" 23 <param argument="-mc" type="text" value="N"
26 label="Replace masking character" 24 label="Replace masking character"
27 help="That is, instead of masking with Ns, use another character. (-mc)" /> 25 help="That is, instead of masking with Ns, use another character" />
28 <param argument="-fullHeader" name="fullheader" type="boolean" truevalue="-fullHeader" falsevalue="" 26 <param argument="-fullHeader" name="fullheader" type="boolean" truevalue="-fullHeader" falsevalue=""
29 label="Use full fasta header." 27 label="Use full fasta header."
30 help="By default, only the word before the first space or tab is used"/> 28 help="By default, only the word before the first space or tab is used"/>
31 </inputs> 29 </inputs>
32 <outputs> 30 <outputs>
33 <data format="fasta" name="output" /> 31 <data name="output" format="fasta" />
34 </outputs> 32 </outputs>
35 <tests> 33 <tests>
36 <test> 34 <test>
37 <param name="input" value="nucBed1.bed" ftype="bed" /> 35 <param name="input" value="nucBed1.bed" ftype="bed" />
38 <param name="fasta" value="nucBed1.fasta" ftype="fasta" /> 36 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
51 <param name="soft" value="True" /> 49 <param name="soft" value="True" />
52 <param name="fullheader" value="True" /> 50 <param name="fullheader" value="True" />
53 <output name="output" file="maskFastaBed_result3.fasta" ftype="fasta" /> 51 <output name="output" file="maskFastaBed_result3.fasta" ftype="fasta" />
54 </test> 52 </test>
55 </tests> 53 </tests>
56 <help> 54 <help><![CDATA[
57 <![CDATA[
58 **What it does** 55 **What it does**
59 56
60 bedtools maskfasta masks sequences in a FASTA file based on intervals defined in a feature file. The headers in the input FASTA file must exactly match the chromosome column in the feature file. This may be useful fro creating your own masked genome file based on custom annotations or for masking all but your target regions when aligning sequence data from a targeted capture experiment. 57 bedtools maskfasta masks sequences in a FASTA file based on intervals defined in a feature file. The headers in the input FASTA file must exactly match the chromosome column in the feature file. This may be useful fro creating your own masked genome file based on custom annotations or for masking all but your target regions when aligning sequence data from a targeted capture experiment.
61 58
62 .. image:: $PATH_TO_IMAGES/maskfasta-glyph.png 59 .. image:: $PATH_TO_IMAGES/maskfasta-glyph.png
63 60
64 @REFERENCES@ 61 @REFERENCES@
65 ]]> 62 ]]></help>
66 </help>
67 <expand macro="citations" /> 63 <expand macro="citations" />
68 </tool> 64 </tool>