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annotate bamToBed.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 b4cf5fca8773
children 7a06bb42dbb1
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678ea22d643d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b822ff8f05f2396fc15bd95a71bc6878503081eb"
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1 <tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1">
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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="requirements">
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7 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
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8 </expand>
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9 <expand macro="stdio" />
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10 <command><![CDATA[
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11 #if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe":
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12 samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' ./input &&
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13 #else
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14 ln -s '${input}' ./input.bam &&
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15 #end if
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16
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17 bedtools bamtobed
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18 $option
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19 $ed_score
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20 $split
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21 #if $tag and str($tag).strip():
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22 -tag '${tag}'
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23 #end if
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24 -i ./input.bam
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25 > '${output}'
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26 ]]></command>
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27 <inputs>
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28 <param name="input" type="data" format="unsorted.bam" label="Convert the following BAM file to BED"/>
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29 <param name="option" type="select" label="What type of BED output would you like">
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30 <option value="">Create a 6-column BED file</option>
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31 <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
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32 <option value="-bedpe">Create a paired-end, BEDPE format</option>
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33 </param>
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34 <expand macro="split" />
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35 <param name="ed_score" argument="-ed" type="boolean" truevalue="-ed" falsevalue="" checked="false"
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36 label="Use alignment's edit-distance for BED score" />
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37 <param argument="-tag" type="text" optional="true"
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38 label="Use other NUMERIC BAM alignment tag as the BED score" />
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39 </inputs>
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40 <outputs>
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41 <data name="output" format="bed" metadata_source="input" label="${input.name} (as BED)"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="input" value="srma_in3.bam" ftype="bam" />
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46 <param name="option" value="" />
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47 <param name="tag" value="" />
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48 <output name="output" file="bamToBed_result1.bed" ftype="bed" />
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49 </test>
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50 <test>
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51 <param name="input" value="srma_in3.bam" ftype="bam" />
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52 <param name="option" value="" />
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53 <param name="tag" value="NM" />
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54 <output name="output" file="bamToBed_result2.bed" ftype="bed" />
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58 **What it does**
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60 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
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61
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62 .. class:: infomark
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63
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64 The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries.
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65 For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp.
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66 However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation).
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67 This is important for RNA-seq and structural variation experiments.
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68
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70 .. class:: warningmark
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71
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72 If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).
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75 @REFERENCES@
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76 ]]></help>
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77 <expand macro="citations" />
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78 </tool>