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annotate convert_characters.xml @ 0:3100886bf698 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:25:21 -0500
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children 81a6c3de5de3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="Convert characters1" name="Convert" version="1.0.0">
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 <description>delimiters to TAB</description>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 <command interpreter="python">convert_characters.py "${input}" "${convert_from}" "${out_file1}"</command>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 <inputs>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5 <param name="convert_from" type="select" label="Convert all">
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 <option value="s">Whitespaces</option>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 <option value="T">Tabs</option>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 <!--<option value="Sp">Spaces</option>-->
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 <option value="Dt">Dots</option>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 <option value="C">Commas</option>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 <option value="D">Dashes</option>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 <option value="U">Underscores</option>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 <option value="P">Pipes</option>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 <option value="Co">Colons</option>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 </param>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 <param format="txt" name="input" type="data" label="in Query"/>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 </inputs>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 <outputs>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 <data format="tabular" name="out_file1" />
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 </outputs>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 <tests>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 <test>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 <param name="convert_from" value="s"/>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 <param name="input" value="1.bed"/>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 <output name="out_file1" file="eq-convert.dat"/>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26 </test>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 <test>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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28 <param name="convert_from" value="s"/>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 <param name="input" value="a.txt"/>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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30 <output name="out_file1" file="a.tab"/>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 </test>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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32 </tests>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33 <help>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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34
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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35 **What it does**
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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36
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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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.
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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38
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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39 -----
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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40
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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41 **Example**
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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42
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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43 - Input file::
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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44
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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45 chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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46 chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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47 chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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48 chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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49
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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50 - Converting all pipe delimiters of the above file to TABs will get::
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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51
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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52 chrX 151283558 151283724 NM_000808_exon_8_0_chrX_151283559_r 0 -
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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53 chrX 151370273 151370486 NM_000808_exon_9_0_chrX_151370274_r 0 -
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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54 chrX 151559494 151559583 NM_018558_exon_1_0_chrX_151559495_f 0 +
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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55 chrX 151564643 151564711 NM_018558_exon_2_0_chrX_151564644_f 0 +
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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56
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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57 </help>
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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58 </tool>