Mercurial > repos > erasmus-medical-center > dr_disco

annotate dr-disco_bam-extract.xml @ 1:9495360713d4 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
author erasmus-medical-center
date Thu, 16 Mar 2017 04:24:23 -0400
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children 173ca9768e22
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9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
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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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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="version_command"/>
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10 <command detect_errors="exit_code"><![CDATA[
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
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11 dr-disco bam-extract
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12 '$region1'
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13 '$region2'
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14 '$output'
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15 '$input_alignment'
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16 ]]></command>
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17 <inputs>
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18 <param name="input_alignment" type="data" format="bam" label="Discordant alignment file of STAR)" />
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19 <param name="region1" type="text" value="chr21:39737183-40035618" label="Genomic region 1" />
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20 <param name="region2" type="text" value="chr21:42834478-42882085" label="Genomic region 2" />
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21 </inputs>
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22 <outputs>
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23 <data name="output" format="bam" label="${tool.name} on ${input_alignment.name}" />
9495360713d4 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
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24 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input_alignment" value="bam_extract.bam" />
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29 <param name="region1" value="chr21:39737183-40035618" />
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30 <param name="region2" value="chr21:42834478-42882085" />
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32 <output name="output" file="bam_extract.bam" />
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33 </test>
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34 <test>
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35 <param name="input_alignment" value="bam_extract.bam" />
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36 <param name="region1" value="chr22:39737183-40035618" />
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37 <param name="region2" value="chr11:42834478-42882085" />
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39 <output name="output" file="bam_extract.empty.bam" />
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40 </test>
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41 </tests>
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43 <help>
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44 Extract reads from two chromosomal positions (and also takes mates with the same name)
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46 Regions are in the format:
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47 chr1:123-546
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48 </help>
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50 <expand macro="citations"/>
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51 </tool>