Mercurial > repos > bgruening > text_processing
annotate unsorted_uniq.xml @ 27:08cdbfffce67 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
| author | bgruening |
|---|---|
| date | Fri, 07 Mar 2025 20:43:41 +0000 |
| parents | f22a309187a3 |
| children |
| rev | line source |
|---|---|
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
parents:
14
diff
changeset
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1 <tool id="tp_sorted_uniq" name="Unique" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 0 | 2 <description>occurrences of each record</description> |
| 4 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
parents:
14
diff
changeset
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6 <expand macro="creator"/> |
| 4 | 7 <expand macro="requirements" /> |
| 8 <version_command>sort --version | head -n 1</version_command> | |
| 9 <command> | |
| 10 <![CDATA[ | |
| 11 sort -u | |
| 12 $ignore_case | |
| 13 $is_numeric | |
| 14 -t ' ' | |
| 15 #if $adv_opts.adv_opts_selector == "advanced": | |
| 16 -k$adv_opts.column_start,$adv_opts.column_end | |
| 17 #end if | |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
parents:
14
diff
changeset
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18 -o '$outfile' |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
parents:
14
diff
changeset
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19 '$infile' |
| 4 | 20 ]]> |
| 0 | 21 </command> |
| 22 <inputs> | |
| 4 | 23 <param name="infile" type="data" format="tabular" label="File to scan for unique values" /> |
| 24 <param name="ignore_case" type="boolean" truevalue="-f" falsevalue="" checked="False" | |
| 25 label="Ignore differences in case when comparing" help="(-f)"/> | |
| 26 <param name="is_numeric" type="boolean" truevalue="-n" falsevalue="" checked="False" | |
| 27 label="Column only contains numeric values" help="(-n)" /> | |
| 0 | 28 <conditional name="adv_opts"> |
| 29 <param name="adv_opts_selector" type="select" label="Advanced Options"> | |
| 4 | 30 <option value="basic" selected="True">Hide Advanced Options</option> |
| 31 <option value="advanced">Show Advanced Options</option> | |
| 0 | 32 </param> |
| 33 <when value="basic" /> | |
| 34 <when value="advanced"> | |
| 4 | 35 <param name="column_start" type="data_column" data_ref="infile" label="Column start" help="Unique on specific column range"/> |
| 36 <param name="column_end" type="data_column" data_ref="infile" label="Column end" help="Unique on specific column range"/> | |
| 0 | 37 </when> |
| 38 </conditional> | |
| 39 </inputs> | |
| 40 <outputs> | |
| 6 | 41 <data name="outfile" format_source="infile" metadata_source="infile"/> |
| 0 | 42 </outputs> |
| 43 <tests> | |
| 44 <test> | |
| 4 | 45 <param name="infile" value="1.bed"/> |
| 46 <param name="is_numeric" value="True"/> | |
| 47 <param name="ignore_case" value="True"/> | |
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08cdbfffce67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents:
26
diff
changeset
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48 <conditional name="adv_opts"> |
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08cdbfffce67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents:
26
diff
changeset
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49 <param name="adv_opts_selector" value="advanced"/> |
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08cdbfffce67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents:
26
diff
changeset
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50 <param name="column_start" value="2"/> |
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08cdbfffce67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents:
26
diff
changeset
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51 <param name="column_end" value="3"/> |
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08cdbfffce67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents:
26
diff
changeset
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52 </conditional> |
| 4 | 53 <output name="outfile" file="unique_results1.bed"/> |
| 0 | 54 </test> |
| 55 </tests> | |
| 56 <help> | |
| 4 | 57 <![CDATA[ |
| 0 | 58 .. class:: infomark |
| 59 | |
| 60 **Syntax** | |
| 61 | |
| 7 | 62 This tool returns all unique lines using the 'sort -u' command. It can be used with unsorted files. |
| 0 | 63 If you need additional options, like grouping or counting your unique results, please use the 'Unique lines from sorted file' tool. |
| 64 | |
| 65 ----- | |
| 66 | |
| 67 .. class:: infomark | |
| 68 | |
| 69 The input file needs to be tab separated. Please convert your file if necessary. | |
| 70 | |
| 71 ----- | |
| 72 | |
| 73 **Example** | |
| 74 | |
| 75 - Input file:: | |
| 7 | 76 |
| 0 | 77 chr1 10 100 gene1 |
| 78 chr1 105 200 gene2 | |
| 79 chr1 10 100 gene1 | |
| 80 chr2 10 100 gene4 | |
| 81 chr2 1000 1900 gene5 | |
| 82 chr3 15 1656 gene6 | |
| 83 chr2 10 100 gene4 | |
| 84 | |
| 85 - Unique lines will result in:: | |
| 86 | |
| 87 chr1 10 100 gene1 | |
| 88 chr1 105 200 gene2 | |
| 89 chr2 10 100 gene4 | |
| 90 chr2 1000 1900 gene5 | |
| 91 chr3 15 1656 gene6 | |
| 92 | |
| 4 | 93 ]]> |
| 0 | 94 </help> |
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7725ab6dab67
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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changeset
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95 <expand macro="citations" /> |
| 0 | 96 </tool> |