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annotate maskFastaBed.xml @ 55:678ea22d643d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b822ff8f05f2396fc15bd95a71bc6878503081eb"
author iuc
date Thu, 06 May 2021 14:14:33 +0000
parents df28283b3778
children 7a06bb42dbb1
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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1 <tool id="bedtools_maskfastabed" name="bedtools MaskFastaBed" version="@TOOL_VERSION@">
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2 <description>use intervals to mask sequences from a FASTA file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command><![CDATA[
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9 bedtools maskfasta
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10 $soft
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11 -mc '${mc}'
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12 -fi '${fasta}'
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13 -bed '${input}'
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14 -fo '${output}'
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15 $fullheader
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16 ]]></command>
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17 <inputs>
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18 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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19 <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file"/>
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20 <param argument="-soft" type="boolean" truevalue="-soft" falsevalue="" checked="false"
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21 label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence"
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22 help="By default, hard-masking (that is, conversion to Ns) is performed" />
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23 <param argument="-mc" type="text" value="N"
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24 label="Replace masking character"
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25 help="That is, instead of masking with Ns, use another character" />
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26 <param argument="-fullHeader" name="fullheader" type="boolean" truevalue="-fullHeader" falsevalue=""
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27 label="Use full fasta header."
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28 help="By default, only the word before the first space or tab is used"/>
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29 </inputs>
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30 <outputs>
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31 <data name="output" format="fasta" />
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="input" value="nucBed1.bed" ftype="bed" />
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36 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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37 <param name="soft" value="False" />
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38 <output name="output" file="maskFastaBed_result1.fasta" ftype="fasta" />
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39 </test>
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40 <test>
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41 <param name="input" value="nucBed1.bed" ftype="bed" />
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42 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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43 <param name="soft" value="True" />
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44 <output name="output" file="maskFastaBed_result2.fasta" ftype="fasta" />
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45 </test>
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46 <test>
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47 <param name="input" value="nucBed1.bed" ftype="bed" />
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48 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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49 <param name="soft" value="True" />
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50 <param name="fullheader" value="True" />
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51 <output name="output" file="maskFastaBed_result3.fasta" ftype="fasta" />
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55 **What it does**
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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.
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59 .. image:: $PATH_TO_IMAGES/maskfasta-glyph.png
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61 @REFERENCES@
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62 ]]></help>
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63 <expand macro="citations" />
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64 </tool>