Mercurial > repos > devteam > convert_characters

annotate convert_characters.xml @ 3:042ed2d0a017 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 20:25:21 -0400
parents 8a53d7f02ce4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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3
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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1 <tool id="Convert characters1" name="Convert" version="1.0.1">
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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2 <description>delimiters to TAB</description>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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3 <requirements>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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4 <requirement type="package" version="3.8">python</requirement>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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5 </requirements>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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6 <command>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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7 python '$__tool_directory__/convert_characters.py'
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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8 '${input}'
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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9 '${convert_from}'
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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10 '${out_file1}'
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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11 </command>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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12 <inputs>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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13 <param name="convert_from" type="select" label="Convert all">
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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14 <option value="s">Whitespaces</option>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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15 <option value="T">Tabs</option>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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16 <!--<option value="Sp">Spaces</option>-->
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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17 <option value="Dt">Dots</option>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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18 <option value="C">Commas</option>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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19 <option value="D">Dashes</option>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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20 <option value="U">Underscores</option>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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21 <option value="P">Pipes</option>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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22 <option value="Co">Colons</option>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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23 </param>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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24 <param format="txt" name="input" type="data" label="in Query"/>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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25 </inputs>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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26 <outputs>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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27 <data format="tabular" name="out_file1" />
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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28 </outputs>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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29 <tests>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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30 <test>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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31 <param name="convert_from" value="s"/>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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32 <param name="input" value="1.bed"/>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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33 <output name="out_file1" file="eq-convert.dat"/>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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34 </test>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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35 <test>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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36 <param name="convert_from" value="s"/>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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37 <param name="input" value="a.txt"/>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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38 <output name="out_file1" file="a.tab"/>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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39 </test>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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40 </tests>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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41 <help>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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42
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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43 **What it does**
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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44
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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45 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.
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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46
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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47 -----
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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48
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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49 **Example**
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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50
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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51 - Input file::
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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52
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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53 chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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54 chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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55 chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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56 chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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57
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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58 - Converting all pipe delimiters of the above file to TABs will get::
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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59
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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60 chrX 151283558 151283724 NM_000808_exon_8_0_chrX_151283559_r 0 -
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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61 chrX 151370273 151370486 NM_000808_exon_9_0_chrX_151370274_r 0 -
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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62 chrX 151559494 151559583 NM_018558_exon_1_0_chrX_151559495_f 0 +
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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63 chrX 151564643 151564711 NM_018558_exon_2_0_chrX_151564644_f 0 +
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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64
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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65 </help>
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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66 </tool>