Mercurial > repos > bgruening > text_processing
annotate unsorted_uniq.xml @ 6:60edf2f8c28f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
| author | bgruening |
|---|---|
| date | Sat, 06 May 2017 13:09:05 -0400 |
| parents | 5314e5d6f040 |
| children | 12615d397df7 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="tp_sorted_uniq" name="Unique" version="@BASE_VERSION@.0"> |
| 2 <description>occurrences of each record</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <version_command>sort --version | head -n 1</version_command> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 sort -u | |
| 11 $ignore_case | |
| 12 $is_numeric | |
| 13 -t ' ' | |
| 14 #if $adv_opts.adv_opts_selector == "advanced": | |
| 15 -k$adv_opts.column_start,$adv_opts.column_end | |
| 16 #end if | |
| 17 -o "$outfile" | |
| 18 "$infile" | |
| 19 ]]> | |
| 20 </command> | |
| 21 <inputs> | |
| 22 <param name="infile" type="data" format="tabular" label="File to scan for unique values" /> | |
| 23 <param name="ignore_case" type="boolean" truevalue="-f" falsevalue="" checked="False" | |
| 24 label="Ignore differences in case when comparing" help="(-f)"/> | |
| 25 <param name="is_numeric" type="boolean" truevalue="-n" falsevalue="" checked="False" | |
| 26 label="Column only contains numeric values" help="(-n)" /> | |
| 27 <conditional name="adv_opts"> | |
| 28 <param name="adv_opts_selector" type="select" label="Advanced Options"> | |
| 29 <option value="basic" selected="True">Hide Advanced Options</option> | |
| 30 <option value="advanced">Show Advanced Options</option> | |
| 31 </param> | |
| 32 <when value="basic" /> | |
| 33 <when value="advanced"> | |
| 34 <param name="column_start" type="data_column" data_ref="infile" label="Column start" help="Unique on specific column range"/> | |
| 35 <param name="column_end" type="data_column" data_ref="infile" label="Column end" help="Unique on specific column range"/> | |
| 36 </when> | |
| 37 </conditional> | |
| 38 </inputs> | |
| 39 <outputs> | |
| 40 <data name="outfile" format_source="infile" metadata_source="infile"/> | |
| 41 </outputs> | |
| 42 <tests> | |
| 43 <test> | |
| 44 <param name="infile" value="1.bed"/> | |
| 45 <param name="is_numeric" value="True"/> | |
| 46 <param name="ignore_case" value="True"/> | |
| 47 <param name="adv_opts_selector" value="advanced"/> | |
| 48 <param name="column_start" value="2"/> | |
| 49 <param name="column_end" value="3"/> | |
| 50 <output name="outfile" file="unique_results1.bed"/> | |
| 51 </test> | |
| 52 </tests> | |
| 53 <help> | |
| 54 <![CDATA[ | |
| 55 .. class:: infomark | |
| 56 | |
| 57 **Syntax** | |
| 58 | |
| 59 This tool returns all unique lines using the 'sort -u' command. It can be used with unsorted files. | |
| 60 If you need additional options, like grouping or counting your unique results, please use the 'Unique lines from sorted file' tool. | |
| 61 | |
| 62 ----- | |
| 63 | |
| 64 .. class:: infomark | |
| 65 | |
| 66 The input file needs to be tab separated. Please convert your file if necessary. | |
| 67 | |
| 68 ----- | |
| 69 | |
| 70 **Example** | |
| 71 | |
| 72 - Input file:: | |
| 73 | |
| 74 chr1 10 100 gene1 | |
| 75 chr1 105 200 gene2 | |
| 76 chr1 10 100 gene1 | |
| 77 chr2 10 100 gene4 | |
| 78 chr2 1000 1900 gene5 | |
| 79 chr3 15 1656 gene6 | |
| 80 chr2 10 100 gene4 | |
| 81 | |
| 82 - Unique lines will result in:: | |
| 83 | |
| 84 chr1 10 100 gene1 | |
| 85 chr1 105 200 gene2 | |
| 86 chr2 10 100 gene4 | |
| 87 chr2 1000 1900 gene5 | |
| 88 chr3 15 1656 gene6 | |
| 89 | |
| 90 @REFERENCES@ | |
| 91 ]]> | |
| 92 </help> | |
|
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60edf2f8c28f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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93 <expand macro="citations" /> |
| 0 | 94 </tool> |