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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
author iuc
date Mon, 29 Jul 2019 08:40:14 -0400
parents c2549832fb33
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c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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1 <tool id="samtools_rmdup" name="RmDup" version="2.0.1">
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2 <description>remove PCR duplicates</description>
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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7 <expand macro="requirements" />
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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11 <command><![CDATA[
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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12 samtools rmdup
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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13 #if str( $bam_paired_end_type.bam_paired_end_type_selector ) == "PE"
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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14 ${bam_paired_end_type.force_se}
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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15 #else:
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16 -s
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17 #end if
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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18 '$input1'
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19 '$output1'
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20 ]]></command>
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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22 <inputs>
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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23 <param name="input1" type="data" format="bam" label="BAM File" />
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24
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25 <conditional name="bam_paired_end_type">
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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26 <param name="bam_paired_end_type_selector" type="select" label="Is this paired-end or single end data">
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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27 <option value="PE" selected="True">BAM is paired-end</option>
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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28 <option value="SE">BAM is single-end (-s)</option>
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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29 </param>
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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30 <when value="PE">
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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31 <param name="force_se" argument="-S" type="boolean" truevalue="-S" falsevalue="" checked="False" label="Treat as single-end"/>
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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32 </when>
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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33 <when value="SE" /> <!-- No extra parameters here -->
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34 </conditional>
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35 </inputs>
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c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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37 <outputs>
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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38 <data name="output1" format="bam" />
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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39 </outputs>
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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41 <tests>
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42 <test>
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43 <param name="input1" value="samtools-rmdup-input1.bam" ftype="bam" />
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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44 <param name="bam_paired_end_type_selector" value="PE" />
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45 <param name="force_se" />
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47 <output name="output1" file="samtools-rmdup-test1.bam" ftype="bam" sort="True" />
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48 </test>
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49 </tests>
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50 <help>
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51 **What it does**
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52
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c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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53 Remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads).
c2549832fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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54 </help>
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55 <expand macro="citations"/>
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56 </tool>