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author thondeboer
date Wed, 16 May 2018 17:02:51 -0400
parents 5bcfac4f8116
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1 <tool id="computeFraglen"
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2 name="computeFraglen"
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3 version="1.0.0"
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4 profile="16.04">
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5 <description>computes empirical fragment length distribution from sample data in BAM format. Creates model file for use in NEAT-genReads</description>
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6 <requirements>
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7 <requirement type="package" version="0.1.19">samtools</requirement>
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8 <requirement type="package">numpy</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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12 samtools view -d $bam_file
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13 | python2 $__tool_directory__/utilities/computeFraglen.py
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param name="bam_file"
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18 type="data"
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19 format="bam"
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20 label="The BAM file to be used to calculate the fragment from [-]"
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21 help="This will be used by SAMTOOLS to convert BAM to SAM as preparation by the computeFraglen tool"
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22 />
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23
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24 </inputs>
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25 <outputs>
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26 <data format="txt"
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27 name="computeGC_modelfile"
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28 from_work_dir="fraglen.p"
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29 label="${os.path.splitext($bam_file.name)[0]}_fraglen.p"
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30 metadata_source="in_type.reference">
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31 </data>
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32
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="bam_file" value="chrMT-PE-VCF-BAM.bam"/>
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37 <output name="computeGC_modelfile" file="chrMT-PE-VCF-BAM-fraglen.p" compare="diff"/>
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38 </test>
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39
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40 </tests>
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41 </tool>