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1 <tool id="ribocount" name="ribocount" version="0.1.0">
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2 <description>Get read counts for all transcripts in an alignment (BAM)
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3 </description>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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4 <requirements>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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5 <requirement type="package" version="0.8.3">pysam</requirement>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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6 </requirements>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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7 <stdio>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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8 <exit_code range="1:" level="fatal" description="Error" />
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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9 </stdio>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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10 <command interpreter="python">../riboplot/ribocount.py
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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11 --ribo_file "${ribo_file}"
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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12 --transcriptome_fasta "${transcriptome_fasta}"
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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13 --read_length "${read_length}"
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14 --read_offset "${read_offset}"
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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15 --html_file "${html_file}"
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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16 --output_path "${html_file.files_path}"
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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17 ## --debug
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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18 </command>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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19 <inputs>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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20 <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/>
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21 <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/>
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22 <param name="read_length" type="integer" label="Read length to consider" value="28"/>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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23 <param name="read_offset" type="integer" label="Offset" value="0"/>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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24 </inputs>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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25 <outputs>
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26 <data format="html" name="html_file" label="ribocount (HTML report)"/>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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27 </outputs>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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28 <help>
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Vimalkumar Velayudhan <vimal@biotechcoder.com>
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29 </help>
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30 </tool>
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