Mercurial > repos > iuc > datamash_transpose
comparison 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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4:ac092723240d | 5:374cb875d38a |
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1 <tool id="datamash_transpose" name="Transpose" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | 1 <tool id="datamash_transpose" name="Transpose" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
2 <description>rows/columns in a tabular file</description> | 2 <description>rows/columns in a tabular file</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <edam_topics> |
7 <expand macro="stdio" /> | 7 <edam_topic>topic_3570</edam_topic> <!-- Pure math / linear algebra --> |
8 </edam_topics> | |
9 <edam_operations> | |
10 <!-- <edam_operation>operation_1234</edam_operation> --> | |
11 </edam_operations> | |
12 <expand macro="requirements"/> | |
13 <expand macro="stdio"/> | |
8 <command><![CDATA[ | 14 <command><![CDATA[ |
9 datamash transpose | 15 #import os |
10 @FIELD_SEPARATOR@ | 16 #set file_size_MB = os.path.getsize(str($in_file)) / (1024 * 1024) |
11 < $in_file > $out_file | 17 #set size_threshold_MB = 1024 |
18 #if $file_size_MB <= $size_threshold_MB: | |
19 datamash transpose @FIELD_SEPARATOR@ < $in_file > $out_file | |
20 #else: | |
21 ## Input matrix is very big: divide and conquer | |
22 ## If the input file is very big, datamash runs out of memory (much earlier than file size ~ available RAM. | |
23 ## Split into managable chunks of row vectors, transpose the chunks and juxtapose column vector chunks. | |
24 #set num_chunks = 1 + int(file_size_MB/size_threshold_MB) | |
25 echo Huge matrix detected, processing in $num_chunks chunks. && | |
26 split -n l/$num_chunks $in_file split_input_ && | |
27 for chunk in \$(ls split_input*); do | |
28 datamash transpose @FIELD_SEPARATOR@ < \$chunk > \${chunk}_transposed; | |
29 done && | |
30 paste split_input_*_transposed > $out_file | |
31 #end if | |
12 ]]></command> | 32 ]]></command> |
13 <expand macro="inputs_outputs" /> | 33 <expand macro="inputs_outputs"/> |
14 <tests> | 34 <tests> |
35 <test expect_num_outputs="1"> | |
36 <param name="in_file" value="datamash_transpose_input.txt"/> | |
37 <output file="datamash_transpose_output.txt" name="out_file"/> | |
38 </test> | |
39 <!-- Test for transposing an extremely big input matrix | |
40 Disabled to keep the repository size reasonable. | |
41 For testing, manually download a pathological in- and output from: | |
42 https://usegalaxy.eu/u/tunc/h/very-big-scrna-matrix | |
43 --> | |
44 <!-- | |
15 <test> | 45 <test> |
16 <param name="in_file" value="datamash_transpose_input.txt" /> | 46 <param name="in_file" value="big.tabular"/> |
17 <output file="datamash_transpose_output.txt" name="out_file" /> | 47 <output file="transposed_big.tabular" name="out_file"/> |
18 </test> | 48 </test> |
49 --> | |
50 <!-- transpose(transpose(A)) = A --> | |
51 <!-- | |
52 <test> | |
53 <param name="in_file" value="transposed_big.tabular"/> | |
54 <output file="big.tabular" name="out_file"/> | |
55 </test> | |
56 --> | |
19 </tests> | 57 </tests> |
20 <help> | 58 <help> |
21 <![CDATA[ | 59 <![CDATA[ |
22 @HELP_HEADER@ | 60 @HELP_HEADER@ |
23 | 61 |
43 HH B3 490 | 81 HH B3 490 |
44 | 82 |
45 @HELP_FOOTER@ | 83 @HELP_FOOTER@ |
46 ]]> | 84 ]]> |
47 </help> | 85 </help> |
86 <expand macro="citation"/> | |
48 </tool> | 87 </tool> |