Mercurial > repos > bgruening > unique
comparison uniq.xml @ 0:4382d742830f draft
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| author | bgruening |
|---|---|
| date | Mon, 26 Aug 2013 04:38:43 -0400 |
| parents | |
| children | 7ce75adb93be |
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| -1:000000000000 | 0:4382d742830f |
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| 1 <tool id="bg_uniq" name="Unique" version="0.3"> | |
| 2 <description>occurrences of each record</description> | |
| 3 <command interpreter='python'> | |
| 4 unique_lines.py | |
| 5 $ignore_case | |
| 6 $is_numeric | |
| 7 #if $adv_opts.adv_opts_selector=="advanced": | |
| 8 $adv_opts.column_start | |
| 9 $adv_opts.column_end | |
| 10 #end if | |
| 11 $outfile | |
| 12 $input | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <param name="input" type="data" format="tabular,text" label="from query" /> | |
| 16 <param name="ignore_case" type="boolean" label="ignore differences in case when comparing" truevalue="-f" falsevalue="false" checked="false" help="ignore differences in case when comparing"/> | |
| 17 <param name="is_numeric" type="boolean" label="column only contains numeric values" truevalue="-n" falsevalue="false" checked="false" help="did the calumn have numeric values"/> | |
| 18 <conditional name="adv_opts"> | |
| 19 <param name="adv_opts_selector" type="select" label="Advanced Options"> | |
| 20 <option value="basic" selected="True">Hide Advanced Options</option> | |
| 21 <option value="advanced">Show Advanced Options</option> | |
| 22 </param> | |
| 23 <when value="basic" /> | |
| 24 <when value="advanced"> | |
| 25 <param name="column_start" label="Column start" type="data_column" data_ref="input" help="Unique on specific column range"/> | |
| 26 <param name="column_end" label="Column end" type="data_column" data_ref="input" help="Unique on specific column range"/> | |
| 27 </when> | |
| 28 </conditional> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data format="input" name="outfile" /> | |
| 32 </outputs> | |
| 33 <tests> | |
| 34 <test> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help> | |
| 38 | |
| 39 .. class:: infomark | |
| 40 | |
| 41 **Syntax** | |
| 42 | |
| 43 This tool returns all unique lines using the 'sort -u' command. | |
| 44 | |
| 45 ----- | |
| 46 | |
| 47 .. class:: infomark | |
| 48 | |
| 49 The input file needs to be tab separated. Please convert your file if necessary. | |
| 50 | |
| 51 ----- | |
| 52 | |
| 53 **Example** | |
| 54 | |
| 55 - Input file:: | |
| 56 | |
| 57 chr1 10 100 gene1 | |
| 58 chr1 105 200 gene2 | |
| 59 chr1 10 100 gene1 | |
| 60 chr2 10 100 gene4 | |
| 61 chr2 1000 1900 gene5 | |
| 62 chr3 15 1656 gene6 | |
| 63 chr2 10 100 gene4 | |
| 64 | |
| 65 - Unique lines will result in:: | |
| 66 | |
| 67 chr1 10 100 gene1 | |
| 68 chr1 105 200 gene2 | |
| 69 chr2 10 100 gene4 | |
| 70 chr2 1000 1900 gene5 | |
| 71 chr3 15 1656 gene6 | |
| 72 | |
| 73 | |
| 74 </help> | |
| 75 </tool> |