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1 <tool id="AGEseq" name="AGEseq">
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2 <description>Analysis of Genome Editing by Sequencing</description>
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3 <command interpreter="perl">AGEseq_web.pl $target $read $mismatch $minAbundance $wtNum $indelNum $output </command>
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4 <inputs>
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5 <param format="txt" name="target" type="data" label="Target File (Reference Table)" help="Select target/reference file."/>
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6 <param format="" name="read" type="data" label="Read file (Sanger or NGS)" help="Select read file in fasta or fastq format." />
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7
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8
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9 <param name="mismatch" type="float" value="0.1" label="Mismatch Rate Cutoff" help="Mismatch rate to filter low quality alignment, default 0.1 (10 %)" />
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10 <param name="minAbundance" type="integer" value="0" label="Abundance Cutoff" help="Cutoff to filter reads with low abundance, default 0" />
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11 <param name="wtNum" type="integer" value="20" label="Numbers of WT-like records to be reported" help="Report top xx WT like records, default 20" />
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12 <param name="indelNum" type="integer" value="50" label="Numbers of records with indel to be reported" help="Report top xx records with indel, default 50" />
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13
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14 </inputs>
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15
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16 <outputs>
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17 <data format="txt" name="output" />
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18 </outputs>
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19
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20
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21 <tests>
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22 <test>
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23 <param name="target" value="targets.txt"/>
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24 <param name="read" value="S2_L001_R1_001.fastq"/>
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25 <output name="out_file1" file="AGEseq_output.txt"/>
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26 </test>
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27 </tests>
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28
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29
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30 <help>
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31 **AGEseq** compares amplicon sequences with expected target sequences and finds the insertion/deletion sites in the amplicon sequences.
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32
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33 Please refer to http://aspendb.uga.edu/downloads or https://github.com/liangjiaoxue/AGEseq for more details.
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34
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35
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36 </help>
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37
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38 </tool> |
