Mercurial > repos > bgruening > text_processing
comparison sorted_uniq.xml @ 19:12615d397df7 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
| author | bgruening |
|---|---|
| date | Thu, 29 Feb 2024 22:15:20 +0000 |
| parents | 74a8bef53a00 |
| children |
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| 18:d698c222f354 | 19:12615d397df7 |
|---|---|
| 1 <tool id="tp_uniq_tool" name="Unique lines" version="@BASE_VERSION@.1"> | 1 <tool id="tp_uniq_tool" name="Unique lines" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 2 <description>assuming sorted input file</description> | 2 <description>assuming sorted input file</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="creator"/> | |
| 6 <expand macro="requirements"> | 7 <expand macro="requirements"> |
| 7 <requirement type="package" version="4.4">sed</requirement> | 8 <requirement type="package" version="4.8">sed</requirement> |
| 8 </expand> | 9 </expand> |
| 9 <version_command>uniq --version | head -n 1</version_command> | 10 <version_command>uniq --version | head -n 1</version_command> |
| 10 <command> | 11 <command> |
| 11 <![CDATA[ | 12 <![CDATA[ |
| 12 uniq | 13 uniq |
| 21 $grouping.count | 22 $grouping.count |
| 22 $grouping.repeated | 23 $grouping.repeated |
| 23 $grouping.uniqueonly | 24 $grouping.uniqueonly |
| 24 #end if | 25 #end if |
| 25 | 26 |
| 26 "$infile" | 27 '$infile' |
| 27 | 28 |
| 28 #if $grouping.grouping_select == 'no' and $grouping.count: | 29 #if $grouping.grouping_select == 'no' and $grouping.count: |
| 29 ## count will print the count with spaces in front of the line and | 30 ## count will print the count with spaces in front of the line and |
| 30 ## with a space (not a tab) after the number, we need to cahnge that | 31 ## with a space (not a tab) after the number, we need to cahnge that |
| 31 | sed -e 's/ *//' -e 's/ /\t/' | 32 | sed -e 's/ *//' -e 's/ /\t/' |
| 32 #end if | 33 #end if |
| 33 > "$outfile" | 34 > '$outfile' |
| 34 ]]> | 35 ]]> |
| 35 </command> | 36 </command> |
| 36 <inputs> | 37 <inputs> |
| 37 <param name="infile" format="tabular" type="data" | 38 <param name="infile" format="tabular" type="data" |
| 38 label="File to scan for unique values" help="Make sure you have sorted this file" /> | 39 label="File to scan for unique values" help="Make sure you have sorted this file" /> |
| 97 | 98 |
| 98 .. class:: infomark | 99 .. class:: infomark |
| 99 | 100 |
| 100 You can sort your file using either the "Sort" tool in "Filter and Sort", or the "Sort" tool in "Unix Tools". | 101 You can sort your file using either the "Sort" tool in "Filter and Sort", or the "Sort" tool in "Unix Tools". |
| 101 | 102 |
| 102 @REFERENCES@ | |
| 103 ]]> | 103 ]]> |
| 104 </help> | 104 </help> |
| 105 <expand macro="citations" /> | 105 <expand macro="citations" /> |
| 106 </tool> | 106 </tool> |