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annotate bamToBed.xml @ 15:b73962f8fcbf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1
author iuc
date Wed, 05 Jul 2017 17:12:00 -0400
parents 607c0576c6ab
children a33db97b220c
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607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
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1 <tool id="bedtools_bamtobed" name="BAM to BED" version="@WRAPPER_VERSION@.0">
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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="1.2">samtools</requirement>
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8 </expand>
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9 <expand macro="stdio" />
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10 <command>
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11 <![CDATA[
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13 #if $input.extension == 'bam' and $option == "-bedpe":
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14 samtools sort -n "${input}" ./input &&
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
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15 #else
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16 ln -s "${input}" ./input.bam &&
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
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17 #end if
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18
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19 bedtools bamtobed
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20 $option
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21 $ed_score
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22 $split
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23 #if $tag and str($tag).strip():
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24 -tag "${tag}"
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25 #end if
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26 -i ./input.bam
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27 > "${output}"
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28 ]]>
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29 </command>
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30 <inputs>
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31 <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
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32 <param name="option" type="select" label="What type of BED output would you like">
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33 <option value="">Create a 6-column BED file</option>
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34 <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
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35 <option value="-bedpe">Create a paired-end, BEDPE format</option>
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36 </param>
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37 <expand macro="split" />
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38 <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false"
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39 label="Use alignment's edit-distance for BED score" help="(-ed)" />
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40 <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"
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41 help="(-tag)"/>
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42 </inputs>
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43 <outputs>
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44 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="input" value="srma_in3.bam" ftype="bam" />
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49 <param name="option" value="" />
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50 <param name="tag" value="" />
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51 <output name="output" file="bamToBed_result1.bed" ftype="bed" />
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52 </test>
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53 <test>
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54 <param name="input" value="srma_in3.bam" ftype="bam" />
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55 <param name="option" value="" />
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56 <param name="tag" value="NM" />
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57 <output name="output" file="bamToBed_result2.bed" ftype="bed" />
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58 </test>
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59 </tests>
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60 <help>
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61 <![CDATA[
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62 **What it does**
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63
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64 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
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65
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66 .. class:: infomark
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67
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68 The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries.
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69 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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70 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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71 This is important for RNA-seq and structural variation experiments.
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74 .. class:: warningmark
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75
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76 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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79 @REFERENCES@
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80 ]]>
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81 </help>
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82 <expand macro="citations" />
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83 </tool>