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author test-svm
date Wed, 08 Aug 2012 19:20:14 -0400
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1 <tool id="kmersvm_seqprofile" name="Sequence Profiles">
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2 <description>provide length, gc content, and repeat fraction of each sequence</description>
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3 <command interpreter="python">scripts/make_profile.py $input $dbkey ${indices_path.fields.path} seq_profile.txt</command>
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4 <inputs>
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5 <param format="interval" name="input" type="data" label="BED File of Regions of interest" />
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6 <validator type="unspecified_build" />
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7 <validator type="dataset_metadata_in_file" filename="nullseq_indices.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are currently unavailable for the specified build." />
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8 <param name="indices_path" type="select" label="Available Datasets">
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9 <options from_file="nullseq_indices.loc">
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10 <column name="dbkey" index="0"/>
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11 <column name="value" index="0"/>
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12 <column name="name" index="1"/>
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13 <column name="path" index="2"/>
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14 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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15 </options>
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16 </param>
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17 </inputs>
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18 <outputs>
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19 <data format="tabular" name="seq_profile.txt" from_work_dir="seq_profile.txt" />
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20 </outputs>
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21 <help>
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22
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23 **What it does**
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24
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25 Takes as input a BED file and the file's corresponding genome build.
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26
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27 Returns length, GC and repeat content information for each interval in bed file.
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28
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29 ----
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30
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31 **Example**
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32
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33 Profile file::
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34
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35 mm9_chr10_6238300_6238926_+ 626 0.525559105431 0.0
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36 mm9_chr10_7757450_7758801_+ 1351 0.451517394523 0.0384900074019
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37 mm9_chr10_8992150_8992551_+ 401 0.411471321696 0.0
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38 mm9_chr10_9265550_9266026_+ 476 0.38025210084 0.0
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39
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40 </help>
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41 </tool>