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This commit is contained in:
Nicola Soranzo
2014-10-28 12:21:00 +01:00
parent a8f6bbc79f
commit 526c2507d7
1 changed files with 59 additions and 59 deletions
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tools/filters/convert_characters.xml
+59 -59
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@@ -1,59 +1,59 @@
<tool id="Convert characters1" name="Convert">
<description>delimiters to TAB</description>
<command interpreter="python">convert_characters.py $input $convert_from $out_file1</command>
<inputs>
<param name="convert_from" type="select" label="Convert all">
<option value="s">Whitespaces</option>
<option value="T">Tabs</option>
<!--<option value="Sp">Spaces</option>-->
<option value="Dt">Dots</option>
<option value="C">Commas</option>
<option value="D">Dashes</option>
<option value="U">Underscores</option>
<option value="P">Pipes</option>
<option value="Co">Colons</option>
<option value="Sc">Semicolons</option>
</param>
<param format="txt" name="input" type="data" label="in Dataset"/>
</inputs>
<outputs>
<data format="tabular" name="out_file1" />
</outputs>
<tests>
<test>
<param name="convert_from" value="s"/>
<param name="input" value="1.bed"/>
<output name="out_file1" file="eq-convert.dat"/>
</test>
<test>
<param name="convert_from" value="s"/>
<param name="input" value="a.txt"/>
<output name="out_file1" file="a.tab"/>
</test>
</tests>
<help>
**What it does**
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.
-----
**Example**
- Input file::
chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+
- Converting all pipe delimiters of the above file to TABs will get::
chrX 151283558 151283724 NM_000808_exon_8_0_chrX_151283559_r 0 -
chrX 151370273 151370486 NM_000808_exon_9_0_chrX_151370274_r 0 -
chrX 151559494 151559583 NM_018558_exon_1_0_chrX_151559495_f 0 +
chrX 151564643 151564711 NM_018558_exon_2_0_chrX_151564644_f 0 +
</help>
</tool>
<tool id="Convert characters1" name="Convert">
<description>delimiters to TAB</description>
<command interpreter="python">convert_characters.py $input $convert_from $out_file1</command>
<inputs>
<param name="convert_from" type="select" label="Convert all">
<option value="s">Whitespaces</option>
<option value="T">Tabs</option>
<!--<option value="Sp">Spaces</option>-->
<option value="Dt">Dots</option>
<option value="C">Commas</option>
<option value="D">Dashes</option>
<option value="U">Underscores</option>
<option value="P">Pipes</option>
<option value="Co">Colons</option>
<option value="Sc">Semicolons</option>
</param>
<param format="txt" name="input" type="data" label="in Dataset"/>
</inputs>
<outputs>
<data format="tabular" name="out_file1" />
</outputs>
<tests>
<test>
<param name="convert_from" value="s"/>
<param name="input" value="1.bed"/>
<output name="out_file1" file="eq-convert.dat"/>
</test>
<test>
<param name="convert_from" value="s"/>
<param name="input" value="a.txt"/>
<output name="out_file1" file="a.tab"/>
</test>
</tests>
<help>
**What it does**
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.
-----
**Example**
- Input file::
chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+
- Converting all pipe delimiters of the above file to TABs will get::
chrX 151283558 151283724 NM_000808_exon_8_0_chrX_151283559_r 0 -
chrX 151370273 151370486 NM_000808_exon_9_0_chrX_151370274_r 0 -
chrX 151559494 151559583 NM_018558_exon_1_0_chrX_151559495_f 0 +
chrX 151564643 151564711 NM_018558_exon_2_0_chrX_151564644_f 0 +
</help>
</tool>