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annotate convert_characters.xml @ 0:64d46676a13e draft

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Uploaded convert_characters tarball.
author devteam
date Tue, 04 Dec 2012 10:55:58 -0500
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children b1cac85bdd7a
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1 <tool id="Convert characters1" name="Convert">
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2 <description>delimiters to TAB</description>
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3 <command interpreter="python">convert_characters.py $input $convert_from $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="Sp">Spaces</option>-->
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9 <option value="Dt">Dots</option>
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10 <option value="C">Commas</option>
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11 <option value="D">Dashes</option>
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12 <option value="U">Underscores</option>
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13 <option value="P">Pipes</option>
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14 <option value="Co">Colons</option>
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15 </param>
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16 <param format="txt" name="input" type="data" label="in Query"/>
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17 </inputs>
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18 <outputs>
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19 <data format="tabular" name="out_file1" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="convert_from" value="s"/>
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24 <param name="input" value="1.bed"/>
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25 <output name="out_file1" file="eq-convert.dat"/>
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26 </test>
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27 <test>
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28 <param name="convert_from" value="s"/>
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29 <param name="input" value="a.txt"/>
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30 <output name="out_file1" file="a.tab"/>
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31 </test>
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32 </tests>
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33 <help>
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34
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35 **What it does**
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36
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37 Converts all delimiters of a specified type into TABs. Consecutive characters are condensed. For example, if columns are separated by 5 spaces they will converted into 1 tab.
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38
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39 -----
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40
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41 **Example**
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42
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43 - Input file::
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44
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45 chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
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46 chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
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47 chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
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48 chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+
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49
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50 - Converting all pipe delimiters of the above file to TABs will get::
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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 </help>
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58 </tool>