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annotate bedToBam.xml @ 64:f6c88d2e9ae5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 9f6bd4c9479f
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f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
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1 <tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>converter</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="bio_tools" />
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <command><![CDATA[
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10 bedtools bedtobam
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11 $bed12
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12 -mapq $mapq
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13 @GENOME_FILE@
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14 -i '$input'
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15 > '$output'
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16 ]]></command>
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17 <inputs>
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18 <param name="input" argument="-i" type="data" format="bed" label="Convert the following BED file to BAM"/>
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19 <param argument="-bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false"
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20 label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format"
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21 help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string"/>
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22 <expand macro="input_conditional_genome_file" />
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23 <param argument="-mapq" type="integer" value="255"
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24 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
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25 </inputs>
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26 <outputs>
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27 <data name="output" format="bam" metadata_source="input" label="${input.name} (as BAM)"/>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input" value="bedToBam1.bed" ftype="bed" />
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32 <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
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33 <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
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34 <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" />
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 **What it does**
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40 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 @REFERENCES@
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43 ]]></help>
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44 <expand macro="citations" />
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45 </tool>