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comparison AGEseq.xml @ 1:fafe271a0842 draft

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Galaxy xml file
author lxue
date Fri, 15 May 2015 16:38:42 -0400
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0:a9c5e846dd76 1:fafe271a0842
1 <tool id="AGEseq" name="AGEseq">
2 <description>Analysis of Genome Editing by Sequencing</description>
3 <command interpreter="perl">AGEseq_web.pl $target $read $mismatch $minAbundance $wtNum $indelNum $output </command>
4 <inputs>
5 <param format="txt" name="target" type="data" label="Target File (Reference Table)" help="Select target/reference file."/>
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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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 %)" />
10 <param name="minAbundance" type="integer" value="0" label="Abundance Cutoff" help="Cutoff to filter reads with low abundance, default 0" />
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" />
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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14 </inputs>
15
16 <outputs>
17 <data format="txt" name="output" />
18 </outputs>
19
20
21 <tests>
22 <test>
23 <param name="target" value="targets.txt"/>
24 <param name="read" value="S2_L001_R1_001.fastq"/>
25 <output name="out_file1" file="AGEseq_output.txt"/>
26 </test>
27 </tests>
28
29
30 <help>
31 **AGEseq** compares amplicon sequences with expected target sequences and finds the insertion/deletion sites in the amplicon sequences.
32
33 Please refer to http://aspendb.uga.edu/downloads or https://github.com/liangjiaoxue/AGEseq for more details.
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36 </help>
37
38 </tool>