[2] | 1 | <tool id="Convert characters1" name="Convert">
|
---|
| 2 | <description>delimiters to TAB</description>
|
---|
| 3 | <command interpreter="python">convert_characters.py $input $convert_from $out_file1</command>
|
---|
| 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>
|
---|