Mercurial > repos > bgruening > barcode_collapse

annotate BarcodeCollapse_pe.xml @ 0:38a8018e57a5 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
author bgruening
date Sat, 11 Jun 2016 10:46:34 -0400
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38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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1 <tool id="barcode_collapse" name="Barcode collapse" version="0.1.0.0">
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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2 <description></description>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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3 <requirements>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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4 <requirement type="package" version="0.8.4">pysam</requirement>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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5 </requirements>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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6 <stdio>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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7 <!-- Anything other than zero is an error -->
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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8 <exit_code range="1:" />
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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9 <exit_code range=":-1" />
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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10 <!-- In case the return code has not been set propery check stderr too -->
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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11 <regex match="Error:" />
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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12 <regex match="Exception:" />
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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13 </stdio>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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14 <command>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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15 <![CDATA[
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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16 ln -s '${input_file}' infile.bam &&
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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17 ln -s '${input_file.metadata.bam_index}' infile.bai &&
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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18
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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19 python $__tool_directory__/barcode_collapse_pe.py
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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20 --bam infile.bam
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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21 --metrics_file '$metrics_file'
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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22 -o '$output'
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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23 ]]>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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24 </command>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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25 <inputs>
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26 <param name="input_file" type="data" format="bam" label="Unsorted bam file to barcode collapse"/>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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27 </inputs>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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28 <outputs>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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29 <data name="output" format="bam"/>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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30 <data name="metrics_file" format="txt"/>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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31 </outputs>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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32 <tests>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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33 <test>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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34 <param name="input_file" value="Trial.bam" ftype="bam"/>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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35 <output name="metrics_file" file="metrics.txt"/>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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36 <output name="output" file="output.bam"/>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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37 </test>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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38 </tests>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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39 <help>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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40 <![CDATA[
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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41 Read in a BAM file where the first 9 nucleotides of the read name are the barcode and merge reads mapped to the same position that have the same barcode.
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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42 Assumes paired end reads are adjacent to each other in the output file (i.e only provide unsorted bams). Also assumes that there are no multimappers in the bam file, if there are multimappers behavior is undefined.
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43 ]]>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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44 </help>
38a8018e57a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse commit cb3ef4df8ea5a705039b32f6959d7513462cfcfc
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45 <citations>
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46 <citation type="doi">10.1038/nmeth.3810</citation>
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47 </citations>
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48 </tool>