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annotate samtools_bedcov.xml @ 3:9149ad20699a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
author iuc
date Mon, 29 Jul 2019 08:47:23 -0400
parents 12749212f61b
children 46c6639921f1
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9149ad20699a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
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1 <tool id="samtools_bedcov" name="BedCov" version="2.0.2">
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2 <description>calculate read depth for a set of genomic intervals</description>
12749212f61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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3 <macros>
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iuc
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4 <import>macros.xml</import>
12749212f61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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5 </macros>
12749212f61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
12749212f61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @PREPARE_IDX_MULTIPLE@
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12749212f61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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12 samtools bedcov
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13 #if $mapq:
9149ad20699a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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14 -Q $mapq
9149ad20699a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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15 #end if
9149ad20699a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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16 $countdel
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17 '${input_bed}'
12749212f61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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18 #for $i in range(len( $input_bams )):
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19 '${i}'
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20 #end for
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21 > '${output}'
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22 ]]></command>
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23 <inputs>
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24 <param name="input_bed" type="data" format="bed" label="Genemic intervals (in BED format)" />
12749212f61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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25 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
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iuc
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26 <param name="mapq" argument="-Q" type="integer" value="" optional="true" label="Minimum MAPQ" help="Only count reads with mapping quality greater than this value" />
9149ad20699a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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27 <param name="countdel" argument="-j" type="boolean" checked="false" truevalue="-j" falsevalue="" label="Exclude deletions and ref skips" help=" Do not include deletions (D) and ref skips (N) in bedcov computation" />
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28 </inputs>
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29 <outputs>
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30 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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35 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
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36 <output name="output" file="samtools_bedcov_out1.tab" />
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37 </test>
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38 <test>
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39 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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40 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
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41 <output name="output" file="samtools_bedcov_out2.tab" />
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42 </test>
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43 <test>
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44 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
9149ad20699a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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45 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
9149ad20699a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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46 <param name="mapq" value="40"/>
9149ad20699a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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47 <output name="output" file="samtools_bedcov_out1.tab" />
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48 </test>
9149ad20699a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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49 <test>
9149ad20699a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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50 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
9149ad20699a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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51 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
9149ad20699a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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52 <param name="countdel" value="-j" />
9149ad20699a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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53 <output name="output" file="samtools_bedcov_out2.tab" />
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54 </test>
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55 </tests>
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56 <help>
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57 **What it does**
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58
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59 Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::
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60
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61 samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]
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62 </help>
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63 <expand macro="citations"/>
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64 </tool>