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annotate multiCov.xml @ 54:b06c53665eb6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
author iuc
date Tue, 23 Mar 2021 20:21:30 +0000
parents df28283b3778
children 7a06bb42dbb1
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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1 <tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@TOOL_VERSION@">
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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="requirements" />
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7 <expand macro="stdio" />
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8 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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9 #for $i, $bam in enumerate($bams):
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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10 ln -s -f '$bam' ${i}.bam &&
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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11 ln -s -f '$bam.metadata.bam_index' ${i}.bam.bai &&
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12 #end for
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13
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14 bedtools multicov
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15 -bed '$input'
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16 -bams
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17 #for $i, $bam in enumerate($bams):
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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18 '${i}.bam'
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19 #end for
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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20 $strand
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21 @OVERLAP@
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22 $reciprocal
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23 $split
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24 -q $q
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25 $duplicate
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26 $failed
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27 $proper
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28 > '$output'
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29 ]]></command>
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30 <inputs>
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31 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sorted @STD_BEDTOOLS_INPUT_LABEL@ file" />
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32 <!-- Additional files, if the user needs more -->
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33 <param argument="-bams" type="data" format="bam" multiple="true" label="BAM file" />
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34
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35 <expand macro="strand2" />
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36 <expand macro="overlap" />
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37 <expand macro="reciprocal" />
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38 <expand macro="split" />
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39 <param argument="-q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" />
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40 <param name="duplicate" argument="-D" type="boolean" truevalue="-D" falsevalue="" checked="false"
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41 label="Include duplicate reads"
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42 help="Default counts non-duplicates only" />
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43 <param name="failed" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="false"
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44 label="Include failed-QC reads"
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45 help="Default counts pass-QC reads only"/>
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46 <param name="proper" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false"
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47 label="Only count proper pairs"
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48 help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field" />
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49 </inputs>
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50 <outputs>
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51 <data name="output" format_source="input" metadata_source="input" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="input" value="multiCov1.bed" ftype="bed" />
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56 <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/>
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57 <param name="q" value="1"/>
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58 <param name="split" value=""/>
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59 <output name="output" file="multiCovBed_result1.bed" ftype="bed" />
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 **What it does**
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65 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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67 @REFERENCES@
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68 ]]></help>
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69 <expand macro="citations" />
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70 </tool>