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1 <tool id="space2underscore_readname" name="Read name modifier" version="1.0.0">
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2 <description>--change space to underscore in the read name column</description>
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3 <command interpreter="python">changespacetounderscore_readname.py $input $output $column_n </command>
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4
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5 <inputs>
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6 <param name="input" type="data" label="Select input" />
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7 <param name="column_n" type="integer" value="6" label="Select column to modify" />
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8 </inputs>
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9 <outputs>
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10 <data format="tabular" name="output" />
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11
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12 </outputs>
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13 <tests>
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14 <!-- Test data with valid values -->
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15 <test>
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16 <param name="input" value="samplefq.snoope"/>
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17 <param name="column_n" value="6"/>
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18 <output name="output" file="samplefq.snoope.new"/>
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19 </test>
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20
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21 </tests>
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22 <help>
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23
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24
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25 .. class:: infomark
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26
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27 **What it does**
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28
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29 The readname produced by the "STR detection" step may contain spaces instead of underscores, which will cause downstream tools that use space as a column delimiter to fail. This tool will help convert space to underscore.
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30 If your input does not have spaces in readname column, this step can be skipped.
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31
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32 **Citation**
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33
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34 When you use this tool, please cite **Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research**
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35
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36 **Input**
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37
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38 The input files can be any tab delimited file.
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39
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40 If this tool is used in STR-FM for STRs profiling, it should be in the same format as output from **STR detection program**. This format contains **length of repeat**, **length of left flanking region**, **length of right flanking region**, **repeat motif**, **hamming (editing) distance**, **read name**, **read sequence**, **read quality score**
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41
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42 **Output**
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43
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44 The same as input format.
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45
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46
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47 </help>
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48 </tool>
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