Mercurial > repos > agordon > datamash_wrapper
changeset 11:687db8c37dcf default tip
remove leftover datamash.xml from merge
| author | Assaf Gordon <agordon@wi.mit.edu> |
|---|---|
| date | Sat, 22 Nov 2014 21:17:57 -0500 |
| parents | ee35019e3cba |
| children | |
| files | datamash.xml |
| diffstat | 1 files changed, 0 insertions(+), 172 deletions(-) [+] |
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--- a/datamash.xml Sat Nov 22 21:13:52 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,172 +0,0 @@ -<tool id="Datamash" name="Datamash" version="1.0.5"> - <description>(operations on tabular data)</description> - - <requirements> - <requirement type="package" version="1.0.5">datamash</requirement> - </requirements> - - <command> - datamash - $header_in - $header_out - $need_sort - $print_full_line - $ignore_case - #if str($grouping)>0 - --group '$grouping' - #end if - #for $oper in $operations - ${oper.op_name} - ${oper.op_column} - #end for - < $in_file > $out_file - </command> - <inputs> - <param format="tabular" name="in_file" type="data" label="Select Input Data" help=""/> - - <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."/> - - <param name="header_in" type="boolean" truevalue="--header-in" falsevalue="" - label="Input file has a header line" help="Mark this if the input file's first line is a header line" /> - - <param name="header_out" type="boolean" truevalue="--header-out" falsevalue="" - label="Print header line" help="Mark this if you want the first line to show the field names" /> - - <param name="need_sort" type="boolean" truevalue="--sort" falsevalue="" - 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." /> - - <param name="print_full_line" type="boolean" truevalue="--full" falsevalue="" - 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." /> - - <param name="ignore_case" type="boolean" truevalue="--ignore-case" falsevalue="" - label="Ignore case when grouping" help="If set, upper/lowercase differences will be ignored when grouping fields." /> - - <repeat name="operations" title="Operation to perform on each group"> - <param name="op_name" type="select" label="Type"> - <option value="count">count</option> - <option value="sum">sum</option> - <option value="min">minimum</option> - <option value="max">maximum</option> - <option value="absmin">Absolute minimum</option> - <option value="absmax">Absolute maximum</option> - <option value="mean">Mean</option> - <option value="pstdev">Population Standard deviantion</option> - <option value="sstdev">Sample Standard deviantion</option> - <option value="median">Median</option> - <option value="q1">1st quartile</option> - <option value="q3">3rd quartile</option> - <option value="iqr">Inter-quartile range</option> - <option value="mad">Median Absolute Deviation</option> - <option value="pvar">Variance (population)</option> - <option value="svar">Variance (sample)</option> - <option value="sskew">Skewness (sample)</option> - <option value="pskew">Skewness (population)</option> - <option value="skurt">Kurtosis (sample)</option> - <option value="pkurt">Kurtosis (population)</option> - <option value="jarque">Jarque-Bera Normality test</option> - <option value="dpo">DAgostino-Pearson Omnibus Normality Test</option> - <option value="mode">Mode</option> - <option value="antimode">Anti-Mode</option> - <option value="unique">Combine all unique values</option> - <option value="collapse">Combine all values</option> - <option value="countunique">Count Unique values</option> - </param> - <param name="op_column" label="On column" type="data_column" data_ref="in_file" /> - </repeat> - </inputs> - - <outputs> - <data format="tabular" name="out_file" /> - </outputs> - - <tests> - <test> - <param name="in_file" value="group_compute_input.txt" /> - <param name="grouping" value="2" /> - <param name="header_in" value="true" /> - <param name="header_out" value="true" /> - <param name="need_sort" value="true" /> - <param name="print_full_line" value="false" /> - <param name="op_column" value="3" /> - <param name="op_name" value="sum" /> - <param name="ignore_case" value="false" /> - <output name="out_file" file="group_compute_output.txt" /> - </test> - </tests> -<help> - -.. 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. - ------ - -**Syntax** - -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. - ------ - -**Example 1** - -- 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:: - - Name Major Score - Bryan Arts 68 - Isaiah Arts 80 - Gabriel Health-Medicine 100 - Tysza Business 92 - Zackery Engineering 54 - ... - ... - -- Grouping the input by the second column (*Major*), and performing operations **mean** and **sample standard deviation** on the third column (*Score*), gives:: - - GroupBy(Major) mean(Score) sstdev(Score) - Arts 68.9474 10.4215 - Business 87.3636 5.18214 - Engineering 66.5385 19.8814 - Health-Medicine 90.6154 9.22441 - Life-Sciences 55.3333 20.606 - Social-Sciences 60.2667 17.2273 - -This sample file is available at http://www.gnu.org/software/datamash . - -**Example 2** - -- Using the UCSC RefSeq Human Gene Track, available at: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz - -- 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:: - - GroupBy(field-13) count(field-2) collapse(field-2) - A1BG 1 NM_130786 - A1BG-AS1 1 NR_015380 - A1CF 6 NM_001198818,NM_001198819,NM_001198820,NM_014576,NM_138932,NM_138933 - A2M 1 NM_000014 - A2M-AS1 1 NR_026971 - A2ML1 2 NM_001282424,NM_144670 - ... - -- 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:: - - GroupBy(field-3) GroupBy(field-4) count(field-2) - chr1 + 2456 - chr1 - 2431 - chr2 + 1599 - chr2 - 1419 - chr3 + 1287 - chr3 - 1249 - ... - ------ - -**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/ - -</help> -</tool>