Mercurial > repos > kyost > atac_primer_tool
annotate filter_bam.xml @ 0:fd3ea97a96bc draft
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author | kyost |
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date | Sat, 28 Apr 2018 15:07:26 -0400 |
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1 <tool id="filter_bam" name="Filter bam files" version="0.1.0"> |
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2 <description> Filters bam files for reads in regions of interest.</description> |
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3 <requirements> |
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4 <requirement type="package" version="1.3">samtools</requirement> |
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5 <requirement type="package" version="2.27.0.0">bedtools</requirement> |
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6 </requirements> |
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7 <stdio> |
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8 <exit_code range="1:" /> |
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9 </stdio> |
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10 <command><![CDATA[ |
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11 #set input_name = str( $input1.name ) |
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12 $__tool_directory__/./filter_bam.bash "$input1" "$input2" "$input3" "$output1" "$output2" "$output3" "$input_name" |
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13 ]]></command> |
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14 <inputs> |
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15 <param type="data" name="input1" format="bam" label="Bam File"/> |
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16 <param type="data" name="input2" format="bed" label="Peak Bed File"/> |
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17 <param type="data" name="input3" format="tabular" label="chrom.sizes"/> |
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18 </inputs> |
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19 <outputs> |
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20 <data name="output1" format="bed" label="Extended Peak File"/> |
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21 <data name="output2" format="bam" label="Filtered Bam File"/> |
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22 <data name="output3" format="tabular" label="Read Counts" /> |
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23 </outputs> |
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24 <tests> |
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25 <test> |
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26 <param name="input1" value="test.bam"/> |
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27 <param name="input2" value="test.bed"/> |
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28 <param name="input3" value="mm9.chrom.sizes.txt"/> |
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29 <output name="output1" file="ext_peak"/> |
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30 <output name="output2" file="test.filter.bam"/> |
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31 <output name="output3" file="test.readcounts.txt"/> |
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32 </test> |
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33 </tests> |
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34 <help><![CDATA[ |
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35 This tools takes a bam file and filters to reads mapping to regions specified by input bed file. Outputs include filtered bam file and count of total numbers of reads in original bam file. |
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36 ]]></help> |
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37 <citations> |
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38 <citation type="doi">doi:10.1038/nmeth.4663</citation> |
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39 </citations> |
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40 </tool> |