Mercurial > repos > iuc > datamash_transpose

annotate datamash-transpose.xml @ 5:374cb875d38a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
author iuc
date Thu, 23 Mar 2023 20:47:02 +0000
parents ba0c40780ecf
children a513e3fbb4c5
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ba0c40780ecf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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1 <tool id="datamash_transpose" name="Transpose" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>rows/columns in a tabular file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
5
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6 <edam_topics>
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7 <edam_topic>topic_3570</edam_topic> <!-- Pure math / linear algebra -->
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8 </edam_topics>
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9 <edam_operations>
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10 <!-- <edam_operation>operation_1234</edam_operation> -->
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11 </edam_operations>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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ba0c40780ecf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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14 <command><![CDATA[
5
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15 #import os
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16 #set file_size_MB = os.path.getsize(str($in_file)) / (1024 * 1024)
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17 #set size_threshold_MB = 1024
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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18 #if $file_size_MB <= $size_threshold_MB:
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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19 datamash transpose @FIELD_SEPARATOR@ < $in_file > $out_file
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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20 #else:
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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21 ## Input matrix is very big: divide and conquer
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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22 ## If the input file is very big, datamash runs out of memory (much earlier than file size ~ available RAM.
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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23 ## Split into managable chunks of row vectors, transpose the chunks and juxtapose column vector chunks.
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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24 #set num_chunks = 1 + int(file_size_MB/size_threshold_MB)
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25 echo Huge matrix detected, processing in $num_chunks chunks. &&
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26 split -n l/$num_chunks $in_file split_input_ &&
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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27 for chunk in \$(ls split_input*); do
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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28 datamash transpose @FIELD_SEPARATOR@ < \$chunk > \${chunk}_transposed;
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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29 done &&
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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30 paste split_input_*_transposed > $out_file
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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31 #end if
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ba0c40780ecf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 206ac70388ea11b168366f1e30bb44157e371c6e"
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32 ]]></command>
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33 <expand macro="inputs_outputs"/>
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34 <tests>
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35 <test expect_num_outputs="1">
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36 <param name="in_file" value="datamash_transpose_input.txt"/>
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37 <output file="datamash_transpose_output.txt" name="out_file"/>
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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38 </test>
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39 <!-- Test for transposing an extremely big input matrix
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40 Disabled to keep the repository size reasonable.
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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41 For testing, manually download a pathological in- and output from:
374cb875d38a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 9edd054251bc74685d627360bb0fbe8ea60fa6a2
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42 https://usegalaxy.eu/u/tunc/h/very-big-scrna-matrix
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43 -->
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44 <!--
0
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45 <test>
5
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46 <param name="in_file" value="big.tabular"/>
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47 <output file="transposed_big.tabular" name="out_file"/>
0
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48 </test>
5
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49 -->
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50 <!-- transpose(transpose(A)) = A -->
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51 <!--
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52 <test>
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53 <param name="in_file" value="transposed_big.tabular"/>
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54 <output file="big.tabular" name="out_file"/>
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55 </test>
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56 -->
0
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57 </tests>
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58 <help>
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59 <![CDATA[
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60 @HELP_HEADER@
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61
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62 **Syntax**
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63
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64 This tools transposes (swaps) rows/columns in a tabular input file.
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65
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66 -----
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67
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68 **Example**
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69
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70 Input file::
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71
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72 Genes NOX1 DcP HH
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73 Sample A1 A2 B3
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74 Counts 514 542 490
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75
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76 Output file::
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77
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78 Genes Sample Counts
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79 NOX1 A1 514
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80 DcP A2 542
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81 HH B3 490
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82
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83 @HELP_FOOTER@
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84 ]]>
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85 </help>
5
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86 <expand macro="citation"/>
0
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87 </tool>