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annotate samtools_rmdup.xml @ 4:9129584416e2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:18:58 -0400
parents bb40e4252392
children
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9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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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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iuc
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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
iuc
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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
iuc
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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
iuc
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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
9129584416e2 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"
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'
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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19 '$output1'
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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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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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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24
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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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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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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" />
9129584416e2 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>
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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41 <tests>
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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42 <test>
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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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" />
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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45 <param name="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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47 <output name="output1" file="samtools-rmdup-test1.bam" ftype="bam" sort="True" />
9129584416e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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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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9129584416e2 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).
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>