Mercurial > repos > devteam > convert_characters
annotate convert_characters.xml @ 2:8a53d7f02ce4 draft
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
| author | devteam |
|---|---|
| date | Tue, 21 Jul 2015 14:17:34 -0400 |
| parents | b1cac85bdd7a |
| children | 042ed2d0a017 |
| rev | line source |
|---|---|
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2
8a53d7f02ce4
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
1
diff
changeset
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1 <tool id="Convert characters1" name="Convert" version="1.0.0"> |
| 0 | 2 <description>delimiters to TAB</description> |
|
1
b1cac85bdd7a
Updated command line format per dev team standards.
Dave B. <dave@bx.psu.edu>
parents:
0
diff
changeset
|
3 <command interpreter="python">convert_characters.py "${input}" "${convert_from}" "${out_file1}"</command> |
| 0 | 4 <inputs> |
| 5 <param name="convert_from" type="select" label="Convert all"> | |
| 6 <option value="s">Whitespaces</option> | |
| 7 <option value="T">Tabs</option> | |
| 8 <!--<option value="Sp">Spaces</option>--> | |
| 9 <option value="Dt">Dots</option> | |
| 10 <option value="C">Commas</option> | |
| 11 <option value="D">Dashes</option> | |
| 12 <option value="U">Underscores</option> | |
| 13 <option value="P">Pipes</option> | |
| 14 <option value="Co">Colons</option> | |
| 15 </param> | |
| 16 <param format="txt" name="input" type="data" label="in Query"/> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format="tabular" name="out_file1" /> | |
| 20 </outputs> | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="convert_from" value="s"/> | |
| 24 <param name="input" value="1.bed"/> | |
| 25 <output name="out_file1" file="eq-convert.dat"/> | |
| 26 </test> | |
| 27 <test> | |
| 28 <param name="convert_from" value="s"/> | |
| 29 <param name="input" value="a.txt"/> | |
| 30 <output name="out_file1" file="a.tab"/> | |
| 31 </test> | |
| 32 </tests> | |
| 33 <help> | |
| 34 | |
| 35 **What it does** | |
| 36 | |
| 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. | |
| 38 | |
| 39 ----- | |
| 40 | |
| 41 **Example** | |
| 42 | |
| 43 - Input file:: | |
| 44 | |
| 45 chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|- | |
| 46 chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|- | |
| 47 chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+ | |
| 48 chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+ | |
| 49 | |
| 50 - Converting all pipe delimiters of the above file to TABs will get:: | |
| 51 | |
| 52 chrX 151283558 151283724 NM_000808_exon_8_0_chrX_151283559_r 0 - | |
| 53 chrX 151370273 151370486 NM_000808_exon_9_0_chrX_151370274_r 0 - | |
| 54 chrX 151559494 151559583 NM_018558_exon_1_0_chrX_151559495_f 0 + | |
| 55 chrX 151564643 151564711 NM_018558_exon_2_0_chrX_151564644_f 0 + | |
| 56 | |
| 57 </help> | |
| 58 </tool> |