annotate bedToBam.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
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1
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1 <tool id="bedtools_bedtobam" name="Convert from BED to BAM" version="@WRAPPER_VERSION@.0">
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2 <description></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>
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9 <![CDATA[
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10 bedtools bedtobam
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11 $bed12
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12 -mapq $mapq
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13 -g $genome
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14 -i '$input'
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15 > '$output'
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/>
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20 <param name="bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false"
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21 label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format"
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22 help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string. (-bed12)"/>
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23 <expand macro="genome" />
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24 <param name="mapq" type="integer" value="255"
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25 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" help="(-mapq)"/>
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26 </inputs>
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27 <outputs>
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28 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input" value="bedToBam1.bed" ftype="bed" />
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33 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
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34 <output name="output" file="bedToBam_result.bam" lines_diff="2" ftype="bam" />
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35 </test>
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36 </tests>
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37 <help>
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38 <![CDATA[
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39 **What it does**
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40
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41 bedToBam converts features in a feature file to BAM format. This is useful as an efficient means of storing large genome annotations in a compact, indexed format for visualization purposes.
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42
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43 @REFERENCES@
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44 ]]>
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45 </help>
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46 <expand macro="citations" />
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47 </tool>