Repository 'vegan_fisher_alpha'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/vegan_fisher_alpha

Changeset 0:a5a453f92273 (2015-12-23)
Next changeset 1:d6b92ca3a9a1 (2016-02-08)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
added:
test-data/output_fisher_alpha.tabular
test-data/vegan_in.tabular
tool_dependencies.xml
vegan_fisher_alpha.xml
vegan_macros.xml
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diff -r 000000000000 -r a5a453f92273 test-data/output_fisher_alpha.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_fisher_alpha.tabular Wed Dec 23 13:55:34 2015 -0500
b
@@ -0,0 +1,2 @@
+"" "x"
+"V2" 2.88807265184344
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diff -r 000000000000 -r a5a453f92273 test-data/vegan_in.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vegan_in.tabular Wed Dec 23 13:55:34 2015 -0500
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@@ -0,0 +1,22 @@
+  3.26 4226 74 P 976         Bacteroidetes
+  0.01 10 2 P 1090         Chlorobi
+  0.90 1163 19 P 1239       Firmicutes
+  0.31 402 12 P 1224       Proteobacteria
+  0.21 275 0 P 201174       Actinobacteria
+  0.02 30 14 P 1117       Cyanobacteria
+  0.01 15 0 P 57723         Acidobacteria
+  0.01 8 1 P 65842         Fibrobacteres
+  0.01 12 0 P 200795       Chloroflexi
+  0.01 8 0 P 142182       Gemmatimonadetes
+  0.01 8 0 P 200783       Aquificae
+  0.01 7 0 P 544448       Tenericutes
+  0.00 6 0 P 203682       Planctomycetes
+  0.00 5 0 P 40117       Nitrospirae
+  0.00 5 1 P 74201         Verrucomicrobia
+  0.00 5 0 P 200918       Thermotogae
+  0.00 2 0 P 32066       Fusobacteria
+  0.00 1 0 P 1297       Deinococcus-Thermus
+  0.00 1 0 P 74152       Elusimicrobia
+  0.00 1 0 P 200930       Deferribacteres
+  0.00 1 0 P 203691       Spirochaetes
+  0.00 1 0 P 28890       Euryarchaeota
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diff -r 000000000000 -r a5a453f92273 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Dec 23 13:55:34 2015 -0500
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@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="vegan" version="2.3-0">
+        <repository changeset_revision="1ab514ba46e7" name="package_r_vegan_2_3_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="R" version="3.2.1">
+        <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
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diff -r 000000000000 -r a5a453f92273 vegan_fisher_alpha.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vegan_fisher_alpha.xml Wed Dec 23 13:55:34 2015 -0500
[
@@ -0,0 +1,47 @@
+<tool id="vegan_fisher_alpha" name="Vegan Fisher Alpha" version="0.0.2">
+    <description>
+        index
+    </description>
+    <macros>
+        <import>vegan_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command><![CDATA[
+        Rscript "${vegan_fisher_alpha_script}"
+    ]]>
+    </command>
+    <configfiles>
+        <configfile name="vegan_fisher_alpha_script"><![CDATA[
+@RSCRIPT_PREAMBLE@
+@RSCRIPT_LOAD_TABULAR_FILE@
+
+write.table( fisher.alpha( input_abundance, MARGIN = ${margin} ), "${output_fisher_alpha}", col.names=NA, sep = "\t")
+    ]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="params_load_tabular_file" />
+        <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output_fisher_alpha" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
+            <param name="species_column" value="6"/>
+            <param name="sample_columns" value="2"/>
+            <param name="margin" value="1"/>
+            <output name="output_fisher_alpha" ftype="tabular" file="output_fisher_alpha.tabular" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+Calculate Diversity index using vegan and selected method.
+        ]]>
+    </help>
+    <citations>
+    </citations>
+</tool>
\ No newline at end of file
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diff -r 000000000000 -r a5a453f92273 vegan_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vegan_macros.xml Wed Dec 23 13:55:34 2015 -0500
[
@@ -0,0 +1,49 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="3.2.1">R</requirement>
+            <requirement type="package" version="2.3-0">vegan</requirement>
+            <yield />
+        </requirements>
+    </xml>
+
+    <xml name="version_command">
+        <version_command><![CDATA[Rscript -e 'library(vegan)' 2>&1 > /dev/null | grep 'This is vegan']]></version_command>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+        </stdio>
+    </xml>
+
+    <xml name="params_load_tabular_file">
+        <param name="input_abundance" type="data" format="tabular" label="File with abundance values for community" help="Rows are samples; columns are species/phyla/community classifier"/>
+        <param name="species_column" label="Group name column" type="data_column" data_ref="input_abundance" value="6" help="Species, phylum, etc"/>
+        <param name="sample_columns" label="Sample count columns" type="data_column" multiple="True" value="2" data_ref="input_abundance" help="Select each column that contains counts"/>
+        <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Input has a header line"/>
+    </xml>
+
+    <token name="@RSCRIPT_LOAD_TABULAR_FILE@"><![CDATA[
+#set $int_species_column = int( str( $species_column ) )
+#set $fixed_sample_columns = []
+#for $sample_col in map( int, str( $sample_columns ).split( "," ) ):
+#assert $sample_col != $int_species_column, "Sample label column and sample count columns must not be the same."
+#silent $fixed_sample_columns.append( str( $sample_col if $sample_col < $int_species_column else $sample_col-1 ) )
+#end for
+input_abundance <- read.delim("${input_abundance}", header=${header}, sep="\t", row.names=${ species_column })
+input_abundance <- t( input_abundance[ c( ${ ",".join( $fixed_sample_columns ) } )] )
+
+]]>
+    </token>
+
+    <token name="@RSCRIPT_PREAMBLE@"><![CDATA[
+options(bitmapType='cairo')## No X11, so we'll use cairo
+library(vegan)
+]]>
+    </token>
+
+    <token name="@VERSION@">2.3-0</token>
+
+</macros>