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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 08:45:55 -0400
parents 9129584416e2
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9129584416e2 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">
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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2 <description>remove PCR duplicates</description>
9129584416e2 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>
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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5 </macros>
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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9129584416e2 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" />
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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8 <expand macro="stdio"/>
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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9 <expand macro="version_command"/>
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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9129584416e2 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[
9129584416e2 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
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13 #if str( $bam_paired_end_type.bam_paired_end_type_selector ) == "PE"
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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14 ${bam_paired_end_type.force_se}
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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15 #else:
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16 -s
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17 #end if
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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18 '$input1'
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19 '$output1'
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20 ]]></command>
9129584416e2 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>
9129584416e2 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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25 <conditional name="bam_paired_end_type">
9129584416e2 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">
9129584416e2 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>
9129584416e2 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>
9129584416e2 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>
9129584416e2 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">
9129584416e2 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"/>
9129584416e2 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>
9129584416e2 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 -->
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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34 </conditional>
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35 </inputs>
9129584416e2 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>
9129584416e2 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" />
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39 </outputs>
9129584416e2 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" />
9129584416e2 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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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).
9129584416e2 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>