Mercurial > repos > iuc > datamash_transpose
changeset 0:6bc5c4e56518 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 1fa5e1a5cfac88256d484ec20c35fc319e6ceb3b
| author | iuc |
|---|---|
| date | Tue, 27 Oct 2015 17:38:08 -0400 |
| parents | |
| children | 1704f8103b97 |
| files | datamash-transpose.xml macros.xml test-data/datamash_reverse_input.txt test-data/datamash_reverse_output.txt test-data/datamash_transpose_input.txt test-data/datamash_transpose_output.txt test-data/group_compute_input.txt test-data/group_compute_output.txt |
| diffstat | 8 files changed, 191 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datamash-transpose.xml Tue Oct 27 17:38:08 2015 -0400 @@ -0,0 +1,45 @@ +<?xml version="1.0"?> +<tool id="datamash_transpose" name="Transpose" version="1.0.6"> + <description>rows/columns in a tabular file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <command><![CDATA[datamash -W transpose < $in_file > $out_file]]></command> + <expand macro="inputs_outputs" /> + <tests> + <test> + <param name="in_file" value="datamash_transpose_input.txt" /> + <output file="datamash_transpose_output.txt" name="out_file" /> + </test> + </tests> + <help> +<![CDATA[ +@HELP_HEADER@ + +**Syntax** + +This tools transposes (swaps) rows/columns in a tabular input file. + +----- + +**Example** + +Input file:: + + Genes NOX1 DcP HH + Sample A1 A2 B3 + Counts 514 542 490 + +Output file:: + + Genes Sample Counts + NOX1 A1 514 + DcP A2 542 + HH B3 490 + +@HELP_FOOTER@ +]]> + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Oct 27 17:38:08 2015 -0400 @@ -0,0 +1,40 @@ +<?xml version="1.0"?> +<macros> + <xml name="inputs_outputs"> + <inputs> + <param format="tabular" help="" label="Input tabular dataset" name="in_file" type="data" /> + <yield /> + </inputs> + <outputs> + <data format="tabular" name="out_file" label="${tool.name} on ${on_string}" /> + </outputs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.0.6">datamash</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code description="Error" level="fatal" range="1:" /> + </stdio> + </xml> + <token name="@HELP_FOOTER@"> +----- + +**GNU Datamash** is a Free and Open Source Software, see more details on the Datamash_ Website. + +**GNU Datamash** is also available as a command-line program, see http://www.gnu.org/software/datamash/download/ . + +For more details about supported statistical operations, see Datamash_ website. + +.. _Datamash: http://www.gnu.org/software/datamash/ + </token> + <token name="@HELP_HEADER@"> +.. class:: infomark + +**TIP:** Input data must be TAB delimited. If the desired dataset does not appear in the input list, use *Text Manipulation->Convert* to convert it to **Tabular** type. + +----- + </token> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/datamash_reverse_input.txt Tue Oct 27 17:38:08 2015 -0400 @@ -0,0 +1,4 @@ +Genes Sample Counts +NOX1 A1 514 +DcP A2 542 +HH B3 490
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/datamash_reverse_output.txt Tue Oct 27 17:38:08 2015 -0400 @@ -0,0 +1,4 @@ +Counts Sample Genes +514 A1 NOX1 +542 A2 DcP +490 B3 HH
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/datamash_transpose_input.txt Tue Oct 27 17:38:08 2015 -0400 @@ -0,0 +1,3 @@ +Genes NOX1 DcP HH +Sample A1 A2 B3 +Counts 514 542 490
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/datamash_transpose_output.txt Tue Oct 27 17:38:08 2015 -0400 @@ -0,0 +1,4 @@ +Genes Sample Counts +NOX1 A1 514 +DcP A2 542 +HH B3 490
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/group_compute_input.txt Tue Oct 27 17:38:08 2015 -0400 @@ -0,0 +1,84 @@ +Name Major Score +Ignatius Engineering 83 +Austin Life-Sciences 91 +Zackery Engineering 54 +Marques Arts 58 +Darren Business 94 +Darius Social-Sciences 51 +Thanh Engineering 53 +Joe'Quann Engineering 75 +Bryan Arts 68 +Devin Engineering 92 +Joseph Social-Sciences 61 +Joshua Life-Sciences 14 +Ja'Won Social-Sciences 37 +Tyreque Arts 74 +Sage Arts 55 +Antonio Engineering 88 +Michael Engineering 39 +Randy Social-Sciences 68 +Dilan Health-Medicine 84 +Omar Engineering 99 +Zachary Arts 80 +Faison Engineering 47 +Angel Health-Medicine 100 +Gabriel Health-Medicine 100 +John Life-Sciences 70 +Leonard Business 87 +Juan Business 79 +Jonathan Health-Medicine 100 +Christopher Life-Sciences 59 +Brandon Life-Sciences 72 +D'Angelo Health-Medicine 90 +Justin Social-Sciences 90 +Israel Health-Medicine 81 +William Arts 46 +David Social-Sciences 69 +Drake Social-Sciences 59 +Drake Social-Sciences 76 +Nathan Arts 71 +Trevon Arts 74 +Aaron Business 83 +Daniel Health-Medicine 91 +Kevin Health-Medicine 100 +Antonio Engineering 56 +Donovan Arts 75 +Kerris Business 82 +Andre Health-Medicine 72 +Dakota Business 83 +Aaron Life-Sciences 58 +Walter Arts 75 +Isaiah Arts 80 +Christian Life-Sciences 67 +Dalton Health-Medicine 100 +Jesse Social-Sciences 32 +Diego Health-Medicine 82 +Nathen Life-Sciences 46 +Anthony Life-Sciences 32 +Christian Business 88 +David Business 92 +Avery Engineering 51 +Paul Arts 63 +Derek Arts 60 +Levi Arts 76 +Lance Social-Sciences 65 +Sonny Engineering 50 +Shawn Arts 65 +Leonardo Engineering 78 +Yeng Life-Sciences 39 +Leroy Social-Sciences 74 +Gurnam Life-Sciences 66 +Fernando Arts 78 +Williams Social-Sciences 62 +Roberto Arts 65 +Teriuse Business 94 +Nathaniel Arts 88 +Chase Social-Sciences 27 +Caleb Business 87 +Tysza Business 92 +Nico Arts 59 +Manuel Social-Sciences 61 +Patrick Health-Medicine 92 +Peter Health-Medicine 86 +Allen Life-Sciences 50 +Joel Social-Sciences 72