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changeset 0:c4611129661b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash commit 8a7a779896ce1b9b296557a2c31bd93f5fbb5462
author iuc
date Wed, 28 Oct 2015 12:46:01 -0400
parents
children 2f3c6f2dcf39
files datamash-ops.xml macros.xml test-data/datamash_reverse_input.txt test-data/datamash_reverse_output.txt test-data/datamash_transpose_input.txt test-data/datamash_transpose_output.txt test-data/group_compute_input.txt test-data/group_compute_output.txt tool_dependencies.xml
diffstat 9 files changed, 299 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datamash-ops.xml	Wed Oct 28 12:46:01 2015 -0400
@@ -0,0 +1,147 @@
+<?xml version="1.0"?>
+<tool id="datamash_ops" name="Datamash" version="1.0.6">
+    <description>(operations on tabular data)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        <![CDATA[
+            datamash
+                $header_in
+                $header_out
+                $need_sort
+                $print_full_line
+                $ignore_case
+                #if str($grouping).strip()
+                --group '$grouping'
+                #end if
+                #for $oper in $operations
+                    ${oper.op_name}
+                    ${oper.op_column}
+                #end for
+                < $in_file > $out_file
+          ]]>
+    </command>
+    <expand macro="inputs_outputs">
+        <param help="Example: to group by the first and fourth fields, use 1,4." label="Group by fields" name="grouping" type="text">
+            <validator message="Invalid value in field. Allowed values are 0-9, space, comma." type="regex">^[0-9, ]*$</validator>
+        </param>
+        <param falsevalue="" help="--header-in" label="Input file has a header line" name="header_in" truevalue="--header-in" type="boolean" />
+        <param falsevalue="" help="--header-out" label="Print header line" name="header_out" truevalue="--header-out" type="boolean" />
+        <param falsevalue="" help="--sort" label="Sort input" name="need_sort" truevalue="--sort" type="boolean" />
+        <param falsevalue="" help="--full" label="Print all fields from input file" name="print_full_line" truevalue="--full" type="boolean" />
+        <param falsevalue="" help="--ignore-case" label="Ignore case when grouping" name="ignore_case" truevalue="--ignore-case" type="boolean" />
+        <repeat default="1" min="1" name="operations" title="Operation to perform on each group">
+            <param label="Type" name="op_name" type="select">
+                <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 data_ref="in_file" label="On column" name="op_column" type="data_column" />
+        </repeat>
+    </expand>
+    <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 file="group_compute_output.txt" name="out_file" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+@HELP_HEADER@
+
+**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
+    ...
+
+@HELP_FOOTER@
+]]>
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Oct 28 12:46:01 2015 -0400
@@ -0,0 +1,40 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="inputs_outputs">
+        <inputs>
+            <param format="tabular" help="" label="Input tabular dataset" name="in_file" type="data" />
+            <yield />
+        </inputs>
+        <outputs>
+            <data format="tabular" name="out_file" label="${tool.name} on ${on_string}" />
+        </outputs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.0.6">datamash</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code description="Error" level="fatal" range="1:" />
+        </stdio>
+    </xml>
+    <token name="@HELP_FOOTER@">
+-----
+
+**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/
+    </token>
+    <token name="@HELP_HEADER@">
+.. 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.
+
+-----
+    </token>
+</macros>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/datamash_reverse_input.txt	Wed Oct 28 12:46:01 2015 -0400
@@ -0,0 +1,4 @@
+Genes	Sample	Counts
+NOX1	A1	514
+DcP	A2	542
+HH	B3	490
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/datamash_reverse_output.txt	Wed Oct 28 12:46:01 2015 -0400
@@ -0,0 +1,4 @@
+Counts	Sample	Genes
+514	A1	NOX1
+542	A2	DcP
+490	B3	HH
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/datamash_transpose_input.txt	Wed Oct 28 12:46:01 2015 -0400
@@ -0,0 +1,3 @@
+Genes	NOX1	DcP	HH
+Sample	A1	A2	B3
+Counts	514	542	490
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/datamash_transpose_output.txt	Wed Oct 28 12:46:01 2015 -0400
@@ -0,0 +1,4 @@
+Genes	Sample	Counts
+NOX1	A1	514
+DcP	A2	542
+HH	B3	490
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/group_compute_input.txt	Wed Oct 28 12:46:01 2015 -0400
@@ -0,0 +1,84 @@
+Name	Major	Score
+Ignatius	Engineering	83
+Austin	Life-Sciences	91
+Zackery	Engineering	54
+Marques	Arts	58
+Darren	Business	94
+Darius	Social-Sciences	51
+Thanh	Engineering	53
+Joe'Quann	Engineering	75
+Bryan	Arts	68
+Devin	Engineering	92
+Joseph	Social-Sciences	61
+Joshua	Life-Sciences	14
+Ja'Won	Social-Sciences	37
+Tyreque	Arts	74
+Sage	Arts	55
+Antonio	Engineering	88
+Michael	Engineering	39
+Randy	Social-Sciences	68
+Dilan	Health-Medicine	84
+Omar	Engineering	99
+Zachary	Arts	80
+Faison	Engineering	47
+Angel	Health-Medicine	100
+Gabriel	Health-Medicine	100
+John	Life-Sciences	70
+Leonard	Business	87
+Juan	Business	79
+Jonathan	Health-Medicine	100
+Christopher	Life-Sciences	59
+Brandon	Life-Sciences	72
+D'Angelo	Health-Medicine	90
+Justin	Social-Sciences	90
+Israel	Health-Medicine	81
+William	Arts	46
+David	Social-Sciences	69
+Drake	Social-Sciences	59
+Drake	Social-Sciences	76
+Nathan	Arts	71
+Trevon	Arts	74
+Aaron	Business	83
+Daniel	Health-Medicine	91
+Kevin	Health-Medicine	100
+Antonio	Engineering	56
+Donovan	Arts	75
+Kerris	Business	82
+Andre	Health-Medicine	72
+Dakota	Business	83
+Aaron	Life-Sciences	58
+Walter	Arts	75
+Isaiah	Arts	80
+Christian	Life-Sciences	67
+Dalton	Health-Medicine	100
+Jesse	Social-Sciences	32
+Diego	Health-Medicine	82
+Nathen	Life-Sciences	46
+Anthony	Life-Sciences	32
+Christian	Business	88
+David	Business	92
+Avery	Engineering	51
+Paul	Arts	63
+Derek	Arts	60
+Levi	Arts	76
+Lance	Social-Sciences	65
+Sonny	Engineering	50
+Shawn	Arts	65
+Leonardo	Engineering	78
+Yeng	Life-Sciences	39
+Leroy	Social-Sciences	74
+Gurnam	Life-Sciences	66
+Fernando	Arts	78
+Williams	Social-Sciences	62
+Roberto	Arts	65
+Teriuse	Business	94
+Nathaniel	Arts	88
+Chase	Social-Sciences	27
+Caleb	Business	87
+Tysza	Business	92
+Nico	Arts	59
+Manuel	Social-Sciences	61
+Patrick	Health-Medicine	92
+Peter	Health-Medicine	86
+Allen	Life-Sciences	50
+Joel	Social-Sciences	72
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/group_compute_output.txt	Wed Oct 28 12:46:01 2015 -0400
@@ -0,0 +1,7 @@
+GroupBy(Major)	sum(Score)
+Arts	1310
+Business	961
+Engineering	865
+Health-Medicine	1178
+Life-Sciences	664
+Social-Sciences	904
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Oct 28 12:46:01 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="datamash" version="1.0.6">
+        <repository changeset_revision="414953c0168d" name="package_datamash_1_0_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>