Mercurial > repos > bgruening > text_processing
annotate sorted_uniq.xml @ 26:f22a309187a3 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
| author | bgruening |
|---|---|
| date | Fri, 16 Aug 2024 10:41:17 +0000 |
| parents | 1e974b82380d |
| children | 08cdbfffce67 |
| 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:
18
diff
changeset
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1 <tool id="tp_uniq_tool" name="Unique lines" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 1 | 2 <description>assuming sorted input file</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:
18
diff
changeset
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6 <expand macro="creator"/> |
| 4 | 7 <expand macro="requirements"> |
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26
f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
parents:
18
diff
changeset
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8 <requirement type="package" version="4.8">sed</requirement> |
| 4 | 9 </expand> |
| 10 <version_command>uniq --version | head -n 1</version_command> | |
| 0 | 11 <command> |
| 4 | 12 <![CDATA[ |
| 13 uniq | |
| 14 #if $skipfields: | |
| 15 -f $skipfields | |
| 16 #end if | |
| 17 $ignorecase | |
| 18 | |
| 19 #if $grouping.grouping_select == 'yes': | |
| 20 --group=$grouping.group | |
| 21 #else: | |
| 22 $grouping.count | |
| 23 $grouping.repeated | |
| 24 $grouping.uniqueonly | |
| 25 #end if | |
| 26 | |
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26
f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
parents:
18
diff
changeset
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27 '$infile' |
| 4 | 28 |
| 29 #if $grouping.grouping_select == 'no' and $grouping.count: | |
| 30 ## count will print the count with spaces in front of the line and | |
| 31 ## with a space (not a tab) after the number, we need to cahnge that | |
| 32 | sed -e 's/ *//' -e 's/ /\t/' | |
| 1 | 33 #end if |
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26
f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
parents:
18
diff
changeset
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34 > '$outfile' |
| 4 | 35 ]]> |
| 0 | 36 </command> |
| 37 <inputs> | |
| 4 | 38 <param name="infile" format="tabular" type="data" |
| 39 label="File to scan for unique values" help="Make sure you have sorted this file" /> | |
| 0 | 40 |
| 4 | 41 <conditional name="grouping"> |
| 42 <param name="grouping_select" type="select" label="Do you want to group each unique group?"> | |
| 43 <option value="no">No</option> | |
| 44 <option value="yes">Yes</option> | |
| 45 </param> | |
| 46 <when value="no"> | |
| 7 | 47 <param name="count" type="boolean" truevalue="-c" falsevalue="" |
| 4 | 48 label="Counting number of occurrences" help="Prefix lines by the number of occurrences. (-c)" /> |
| 7 | 49 <param name="repeated" type="boolean" truevalue="-d" falsevalue="" |
| 4 | 50 label="Only print duplicate lines" help="(-d)"/> |
| 51 <param name="uniqueonly" type="boolean" checked="True" truevalue="-u" falsevalue="" | |
| 52 label="Only print unique lines" help="(-u)" /> | |
| 53 </when> | |
| 54 <when value="yes"> | |
| 6 | 55 <param name="group" type="select" |
| 4 | 56 label="Output all lines, and delimit each unique group" help="(--group)"> |
| 57 <option value="">No grouping at all</option> | |
| 58 <option value="separate">Separate unique groups with a single delimiter</option> | |
| 59 <option value="prepend">Output a delimiter before each group of unique items</option> | |
| 60 <option value="append">Output a delimiter after each group of unique items</option> | |
| 61 <option value="both">Output a delimiter around each group of unique items</option> | |
| 62 </param> | |
| 63 </when> | |
| 64 </conditional> | |
| 65 | |
| 7 | 66 <param name="ignorecase" type="boolean" truevalue="-i" falsevalue="" |
| 4 | 67 label="Ignore differences in case when comparing" help="(-i)"/> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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7
diff
changeset
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68 <param name="skipfields" type="integer" value="0" |
| 4 | 69 label="Avoid comparing the first N fields" help="Use zero to start from the first field. (-f)" /> |
| 0 | 70 </inputs> |
| 71 <outputs> | |
| 6 | 72 <data name="outfile" format_source="infile" metadata_source="infile"/> |
| 0 | 73 </outputs> |
| 4 | 74 <tests> |
| 75 <test> | |
| 76 <param name="infile" value="sorted_uniq1.tabular" /> | |
| 77 <param name="grouping_select" value="no"/> | |
| 78 <param name="count" value="True"/> | |
| 79 <param name="ignorecase" value="True"/> | |
| 80 <param name="uniqueonly" value="True"/> | |
| 81 <output name="outfile" file="sorted_uniq_results1.tabular" /> | |
| 82 </test> | |
| 83 <test> | |
| 84 <param name="infile" value="sorted_uniq1.tabular" /> | |
| 85 <param name="ignorecase" value="True"/> | |
| 86 <param name="grouping_select" value="yes"/> | |
| 87 <param name="group" value="separate"/> | |
| 88 <output name="outfile" file="sorted_uniq_results2.tabular" /> | |
| 89 </test> | |
| 90 </tests> | |
| 0 | 91 <help> |
| 4 | 92 <![CDATA[ |
| 0 | 93 This tool takes a sorted file and look for lines that are unique. |
| 94 | |
| 95 .. class:: warningmark | |
| 96 | |
| 97 Please make sure your file is sorted, or else this tool will give you an erroneous output. | |
| 98 | |
| 99 .. class:: infomark | |
| 100 | |
| 101 You can sort your file using either the "Sort" tool in "Filter and Sort", or the "Sort" tool in "Unix Tools". | |
| 102 | |
| 4 | 103 ]]> |
| 0 | 104 </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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105 <expand macro="citations" /> |
| 0 | 106 </tool> |