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annotate samtools_bedcov.xml @ 3:e371922c38e8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:15:55 -0400
parents 4f7acd7af617
children b7ab754899d5
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e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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1 <tool id="samtools_bedcov" name="BedCov" version="2.0.1">
e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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2 <description>calculate read depth for a set of genomic intervals</description>
e371922c38e8 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>
e371922c38e8 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>
e371922c38e8 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"/>
e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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7 <expand macro="stdio"/>
e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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10 ## Ensure simlinks have unique filenames
e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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11 #for $i, $bam in enumerate( $input_bams ):
e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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12 ln -s -f '${bam}' '${i}.bam' &&
e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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13 ln -s -f '${bam.metadata.bam_index}' '${i}.bam.bai' &&
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14 #end for
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e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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16 samtools bedcov
e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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17 '${input_bed}'
e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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18 #for $i in range(len( $input_bams )):
e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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19 '${i}.bam'
e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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20 #end for
e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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21 > '${output}'
e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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22 ]]></command>
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23 <inputs>
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e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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24 <param name="input_bed" type="data" format="bed" label="Genemic intervals (in BED format)" />
e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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25 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
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26 </inputs>
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27 <outputs>
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e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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28 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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33 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
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34 <output name="output" file="samtools_bedcov_out1.tab" />
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35 </test>
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36 <test>
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37 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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38 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
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39 <output name="output" file="samtools_bedcov_out2.tab" />
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40 </test>
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41 </tests>
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42 <help>
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43 **What it does**
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44
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45 Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::
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46
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47 samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]
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48 </help>
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e371922c38e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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49 <expand macro="citations"/>
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50 </tool>