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1 <tool id="convertdelimiter" name="Convert">
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2 <description>delimiters</description>
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3 <command interpreter="python">replace_delimiter.py $input $convert_from $convert_to $out_file1</command>
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4 <inputs>
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5 <param name="convert_from" type="select" label="Convert all">
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6 <option value="s">Whitespaces</option>
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7 <option value="T">Tabs</option>
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8 <option value="Dt">Dots</option>
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9 <option value="C">Commas</option>
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10 <option value="D">Dashes</option>
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11 <option value="U">Underscores</option>
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12 <option value="P">Pipes</option>
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13 <option value="Co">Colons</option>
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14 <option value="Sc">Semicolons</option>
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15 </param>
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16 <param format="txt" name="input" type="data" label="in Dataset"/>
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17 <param name="convert_to" type="select" label="to ">
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18 <option value="s">Whitespaces</option>
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19 <option value="T">Tabs</option>
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20 <option value="Dt">Dots</option>
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21 <option value="C">Commas</option>
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22 <option value="D">Dashes</option>
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23 <option value="U">Underscores</option>
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24 <option value="P">Pipes</option>
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25 <option value="Co">Colons</option>
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26 <option value="Sc">Semicolons</option>
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27 </param>
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28 </inputs>
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29 <outputs>
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30 <data format="tabular" name="out_file1" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="convert_from" value="P"/>
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35 <param name="input" value="replace_delimiter_input.tsv" ftype="tabular"/>
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36 <param name="convert_to" value="C"/>
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37 <output name="out_file1" file="replace_delimiter_output.csv"/>
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38 </test>
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39 </tests>
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40 <help>
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41
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42 **What it does**
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43
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44 Converts all delimiters of a specified type into a specified delimiter(Dots, Commas, Dashes, Underscores, Pipes, Colons, Semicolons).
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45 Tool and code borrowed from convert_delimiter tool(distributed with Galaxy).
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46 -----
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47
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48 **Example**
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49
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50 - Input file:
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51
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52 chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
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53 chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
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54 chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
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55 chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+
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56
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57 - Converting all pipe delimiters of the above file to Commas will get::
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58
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59 chrX,151283558,151283724,NM_000808_exon_8_0_chrX_151283559_r,0,-
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60 chrX,151370273,151370486,NM_000808_exon_9_0_chrX_151370274_r,0,-
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61 chrX,151559494,151559583,NM_018558_exon_1_0_chrX_151559495_f,0,+
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62 chrX,151564643,151564711,NM_018558_exon_2_0_chrX_151564644_f,0,+
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63
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64 </help>
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65 </tool>
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