Mercurial > repos > agordon > compute_wrapper
annotate compute.xml @ 1:b8e386e9fd0b draft
Update package dependencies
| author | Assaf Gordon <assafgordon@gmail.com> |
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| date | Sat, 22 Mar 2014 16:23:47 -0400 |
| parents | ea8ec99cae2c |
| children | 849d3bd2897c |
| rev | line source |
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Assaf Gordon <assafgordon@gmail.com>
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1 <tool id="GroupCompute" name="Group and Compute" version="1.0.3"> |
| 0 | 2 <description>operations on tabular data.</description> |
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Assaf Gordon <assafgordon@gmail.com>
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3 |
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b8e386e9fd0b
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4 <requirements> |
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b8e386e9fd0b
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5 <requirement type="package" version="1.0.3">compute</requirement> |
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6 </requirements> |
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b8e386e9fd0b
Update package dependencies
Assaf Gordon <assafgordon@gmail.com>
parents:
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7 |
| 0 | 8 <command> |
| 9 compute | |
| 10 $header_in | |
| 11 $header_out | |
| 12 $need_sort | |
| 13 $print_full_line | |
| 14 $ignore_case | |
| 15 #if str($grouping)>0 | |
| 16 --group '$grouping' | |
| 17 #end if | |
| 18 -T | |
| 19 #for $oper in $operations | |
| 20 ${oper.op_name} | |
| 21 ${oper.op_column} | |
| 22 #end for | |
| 23 < $in_file > $out_file | |
| 24 </command> | |
| 25 <inputs> | |
| 26 <param format="tabular" name="in_file" type="data" label="Select Input Data" help=""/> | |
| 27 | |
| 28 <param name="grouping" label="Group by fields" type="text" help="Example: 1,4 - To group by the first and fourth fields. Leave empty to perform operation on entire file as one group."/> | |
| 29 | |
| 30 <param name="header_in" type="boolean" truevalue="--header-in" falsevalue="" | |
| 31 label="Input file has a header line" help="Mark this if the input file's first line is a header line" /> | |
| 32 | |
| 33 <param name="header_out" type="boolean" truevalue="--header-out" falsevalue="" | |
| 34 label="Print header line" help="Mark this if you want the first line to show the field names" /> | |
| 35 | |
| 36 <param name="need_sort" type="boolean" truevalue="--sort" falsevalue="" | |
| 37 label="Sort input" help="Mark if the input file is not sorted. If the input file is already sorted, unmark this option to reduce computing time." /> | |
| 38 | |
| 39 <param name="print_full_line" type="boolean" truevalue="--full" falsevalue="" | |
| 40 label="Print all fields from input file" help="If set, all input fields will be printed. If unset, only fields used for grouping will be printed." /> | |
| 41 | |
| 42 <param name="ignore_case" type="boolean" truevalue="--ignore-case" falsevalue="" | |
| 43 label="Ignore case when grouping" help="If set, upper/lowercase differences will be ignored when grouping fields." /> | |
| 44 | |
| 45 <repeat name="operations" title="Operation to perform on each group"> | |
| 46 <param name="op_name" type="select" label="Type"> | |
| 47 <option value="count">count</option> | |
| 48 <option value="sum">sum</option> | |
| 49 <option value="min">minimum</option> | |
| 50 <option value="max">maximum</option> | |
| 51 <option value="absmin">Absolute minimum</option> | |
| 52 <option value="absmax">Absolute maximum</option> | |
| 53 <option value="mean">Mean</option> | |
| 54 <option value="median">Median</option> | |
| 55 <option value="mode">Mode</option> | |
| 56 <option value="antimode">Anti-Mode</option> | |
| 57 <option value="pstdev">Population Standard deviantion</option> | |
| 58 <option value="sstdev">Sample Standard deviantion</option> | |
| 59 <option value="unique">Combine all unique values</option> | |
| 60 <option value="collapse">Combine all values</option> | |
| 61 <option value="countunique">Count Unique values</option> | |
| 62 </param> | |
| 63 <param name="op_column" label="On column" type="data_column" data_ref="in_file" /> | |
| 64 </repeat> | |
| 65 </inputs> | |
| 66 | |
| 67 <outputs> | |
| 68 <data format="tabular" name="out_file" /> | |
| 69 </outputs> | |
| 70 | |
| 71 <tests> | |
| 72 <test> | |
| 73 <param name="in_file" value="group_compute_input.txt" /> | |
| 74 <param name="grouping" value="2" /> | |
| 75 <param name="header_in" value="true" /> | |
| 76 <param name="header_out" value="true" /> | |
| 77 <param name="need_sort" value="true" /> | |
| 78 <param name="print_full_line" value="false" /> | |
| 79 <param name="op_column" value="3" /> | |
| 80 <param name="op_name" value="sum" /> | |
| 81 <param name="ignore_case" value="false" /> | |
| 82 <output name="out_file" file="group_compute_output.txt" /> | |
| 83 </test> | |
| 84 </tests> | |
| 85 <help> | |
| 86 | |
| 87 .. class:: infomark | |
| 88 | |
| 89 **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. | |
| 90 | |
| 91 ----- | |
| 92 | |
| 93 **Syntax** | |
| 94 | |
| 95 This tools performs common operations (such as summing, counting, mean, standard-deviation) on input file, based on tabular data. The tool can also optionaly group the input based on a given field. | |
| 96 | |
| 97 ----- | |
| 98 | |
| 99 **Example 1** | |
| 100 | |
| 101 - Find the average score in statistics course of college students, grouped by their college major. The input file has three fields (Name,Major,Score) and a header line:: | |
| 102 | |
| 103 Name Major Score | |
| 104 Bryan Arts 68 | |
| 105 Isaiah Arts 80 | |
| 106 Gabriel Health-Medicine 100 | |
| 107 Tysza Business 92 | |
| 108 Zackery Engineering 54 | |
| 109 ... | |
| 110 ... | |
| 111 | |
| 112 - Grouping the input by the second column (*Major*), and performing operations **mean** and **sample standard deviation** on the third column (*Score*), gives:: | |
| 113 | |
| 114 GroupBy(Major) mean(Score) sstdev(Score) | |
| 115 Arts 68.9474 10.4215 | |
| 116 Business 87.3636 5.18214 | |
| 117 Engineering 66.5385 19.8814 | |
| 118 Health-Medicine 90.6154 9.22441 | |
| 119 Life-Sciences 55.3333 20.606 | |
| 120 Social-Sciences 60.2667 17.2273 | |
| 121 | |
| 122 This sample file is available at http://agordon.github.io/compute/examples.html . | |
| 123 | |
| 124 **Example 2** | |
| 125 | |
| 126 - Using the UCSC RefSeq Human Gene Track, available at: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz | |
| 127 | |
| 128 - List the number and identifiers of isoforms per gene. The gene identifier is in column 13, the isoform/transcript identifier is in column 2. Grouping by column 13 and performing **count** and **Combine all values** on column 2, gives:: | |
| 129 | |
| 130 GroupBy(field-13) count(field-2) collapse(field-2) | |
| 131 A1BG 1 NM_130786 | |
| 132 A1BG-AS1 1 NR_015380 | |
| 133 A1CF 6 NM_001198818,NM_001198819,NM_001198820,NM_014576,NM_138932,NM_138933 | |
| 134 A2M 1 NM_000014 | |
| 135 A2M-AS1 1 NR_026971 | |
| 136 A2ML1 2 NM_001282424,NM_144670 | |
| 137 ... | |
| 138 | |
| 139 - Count how many transcripts are listed for each chromosome and strand. Chromosome is on column 3, Strand is in column 4. Transcript identifiers are in column 2. Grouping by columns **3,4** and performing operation **count** on column 2, gives:: | |
| 140 | |
| 141 GroupBy(field-3) GroupBy(field-4) count(field-2) | |
| 142 chr1 + 2456 | |
| 143 chr1 - 2431 | |
| 144 chr2 + 1599 | |
| 145 chr2 - 1419 | |
| 146 chr3 + 1287 | |
| 147 chr3 - 1249 | |
| 148 ... | |
| 149 | |
| 150 ----- | |
| 151 | |
| 152 **Compute** is an open-sourced program, see more details on the Compute_ Website. | |
| 153 | |
| 154 **Compute** is also available as a command-line program, see http://agordon.github.io/compute/examples.html . | |
| 155 | |
| 156 .. _Compute: http://agordon.github.io/compute/ | |
| 157 | |
| 158 </help> | |
| 159 </tool> |