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annotate multiCov.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 539958feb49c
children
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1d0a0d6a78b1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
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1 <tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>counts coverage from multiple BAMs at specific intervals</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 #for $i, $bam in enumerate($bams):
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11 ln -s -f '$bam' ${i}.bam &&
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12 ln -s -f '$bam.metadata.bam_index' ${i}.bam.bai &&
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13 #end for
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14
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15 bedtools multicov
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16 -bed '$input'
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17 -bams
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18 #for $i, $bam in enumerate($bams):
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19 '${i}.bam'
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20 #end for
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21 $strand
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22 @OVERLAP@
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23 $reciprocal
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24 $split
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25 -q $q
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26 $duplicate
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27 $failed
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28 $proper
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29 > '$output'
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30 ]]></command>
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31 <inputs>
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32 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sorted @STD_BEDTOOLS_INPUT_LABEL@ file" />
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33 <!-- Additional files, if the user needs more -->
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34 <param argument="-bams" type="data" format="bam" multiple="true" label="BAM file" />
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35
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36 <expand macro="strand2" />
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37 <expand macro="overlap" />
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38 <expand macro="reciprocal" />
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39 <expand macro="split" />
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40 <param argument="-q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" />
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41 <param name="duplicate" argument="-D" type="boolean" truevalue="-D" falsevalue="" checked="false"
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42 label="Include duplicate reads"
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43 help="Default counts non-duplicates only" />
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44 <param name="failed" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="false"
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45 label="Include failed-QC reads"
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46 help="Default counts pass-QC reads only"/>
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47 <param name="proper" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false"
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48 label="Only count proper pairs"
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49 help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field" />
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50 </inputs>
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51 <outputs>
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52 <data name="output" format_source="input" metadata_source="input" />
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="input" value="multiCov1.bed" ftype="bed" />
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57 <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/>
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58 <param name="q" value="1"/>
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59 <param name="split" value="false"/>
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60 <output name="output" file="multiCovBed_result1.bed" ftype="bed" />
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64 **What it does**
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66 bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file.
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68 @REFERENCES@
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69 ]]></help>
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70 <expand macro="citations" />
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71 </tool>