Mercurial > repos > iuc > datamash_transpose
view datamash-transpose.xml @ 5:374cb875d38a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
author | iuc |
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date | Thu, 23 Mar 2023 20:47:02 +0000 |
parents | ba0c40780ecf |
children | a513e3fbb4c5 |
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<tool id="datamash_transpose" name="Transpose" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>rows/columns in a tabular file</description> <macros> <import>macros.xml</import> </macros> <edam_topics> <edam_topic>topic_3570</edam_topic> <!-- Pure math / linear algebra --> </edam_topics> <edam_operations> <!-- <edam_operation>operation_1234</edam_operation> --> </edam_operations> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ #import os #set file_size_MB = os.path.getsize(str($in_file)) / (1024 * 1024) #set size_threshold_MB = 1024 #if $file_size_MB <= $size_threshold_MB: datamash transpose @FIELD_SEPARATOR@ < $in_file > $out_file #else: ## Input matrix is very big: divide and conquer ## If the input file is very big, datamash runs out of memory (much earlier than file size ~ available RAM. ## Split into managable chunks of row vectors, transpose the chunks and juxtapose column vector chunks. #set num_chunks = 1 + int(file_size_MB/size_threshold_MB) echo Huge matrix detected, processing in $num_chunks chunks. && split -n l/$num_chunks $in_file split_input_ && for chunk in \$(ls split_input*); do datamash transpose @FIELD_SEPARATOR@ < \$chunk > \${chunk}_transposed; done && paste split_input_*_transposed > $out_file #end if ]]></command> <expand macro="inputs_outputs"/> <tests> <test expect_num_outputs="1"> <param name="in_file" value="datamash_transpose_input.txt"/> <output file="datamash_transpose_output.txt" name="out_file"/> </test> <!-- Test for transposing an extremely big input matrix Disabled to keep the repository size reasonable. For testing, manually download a pathological in- and output from: https://usegalaxy.eu/u/tunc/h/very-big-scrna-matrix --> <!-- <test> <param name="in_file" value="big.tabular"/> <output file="transposed_big.tabular" name="out_file"/> </test> --> <!-- transpose(transpose(A)) = A --> <!-- <test> <param name="in_file" value="transposed_big.tabular"/> <output file="big.tabular" 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> <expand macro="citation"/> </tool>