Mercurial > repos > erasmus-medical-center > dr_disco

annotate dr-disco_bam-extract.xml @ 5:76a3992021c1 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit f6f9296f2774ba81f81f57d5f80d597d008e6a1c
author erasmus-medical-center
date Thu, 14 Sep 2017 05:09:34 -0400
parents 5348cfd3ba5c
children 922b52cf9b35
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1 <tool id="dr_disco_bam_extract" name="Dr. Disco (bam-extract)" version="@TOOL_VERSION@-g0">
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2 <description>Extracts reads from two targeted regions</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="version_command"/>
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11 <command detect_errors="exit_code"><![CDATA[
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12 dr-disco bam-extract
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13 '$region1'
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14 '$region2'
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15 '$input_alignment'
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16 '$output'
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17 ]]></command>
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19 <inputs>
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20 <param name="input_alignment" type="data" format="bam" label="Discordant alignment file of STAR)" />
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21 <param name="region1" type="text" value="chr21:39737183-40035618" label="Genomic region 1" />
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22 <param name="region2" type="text" value="chr21:42834478-42882085" label="Genomic region 2" />
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23 </inputs>
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25 <outputs>
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26 <data name="output" format="bam" label="${tool.name} on ${input_alignment.name}" />
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27 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input_alignment" value="bam_extract.bam" />
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32 <param name="region1" value="chr21:39737183-40035618" />
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33 <param name="region2" value="chr21:42834478-42882085" />
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35 <output name="output" file="bam_extract.bam" />
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36 </test>
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37 <test>
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38 <param name="input_alignment" value="bam_extract.bam" />
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39 <param name="region1" value="chr22:39737183-40035618" />
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40 <param name="region2" value="chr11:42834478-42882085" />
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42 <output name="output" file="bam_extract.empty.bam" />
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43 </test>
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44 </tests>
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45
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46 <help><![CDATA[
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48 **What it does**
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50 Extract reads that have their mate within one of two chromosomal positions (and also takes mates that correspond to these reads)
1
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52 Regions are in the format:
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53 chr1:123-546
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54 ]]></help>
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56 <expand macro="citations"/>
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57 </tool>