Mercurial > repos > iuc > vegan_rarefaction

changeset 2:b0d5976540e3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
author iuc
date Fri, 07 Sep 2018 11:31:02 -0400
parents dd2705a31239
children af1211ed6c8e
files macros.xml test-data/output_diversity_index.tabular test-data/output_fisher_alpha.tabular tool_dependencies.xml vegan_macros.xml vegan_rarefaction.xml
diffstat 6 files changed, 58 insertions(+), 64 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Sep 07 11:31:02 2018 -0400
@@ -0,0 +1,48 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">r-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="@TOOL_VERSION@">2.4-3</token>
+
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_diversity_index.tabular	Fri Sep 07 11:31:02 2018 -0400
@@ -0,0 +1,2 @@
+	x
+1	1.020620870138
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_fisher_alpha.tabular	Fri Sep 07 11:31:02 2018 -0400
@@ -0,0 +1,2 @@
+	x
+V2	2.86498950425242
--- a/tool_dependencies.xml	Mon Feb 08 15:24:42 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?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>
--- a/vegan_macros.xml	Mon Feb 08 15:24:42 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-<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>
--- a/vegan_rarefaction.xml	Mon Feb 08 15:24:42 2016 -0500
+++ b/vegan_rarefaction.xml	Fri Sep 07 11:31:02 2018 -0400
@@ -1,9 +1,9 @@
-<tool id="vegan_rarefaction" name="Vegan Rarefaction" version="0.0.3">
+<tool id="vegan_rarefaction" name="Vegan Rarefaction" version="@TOOL_VERSION@">
     <description>
         curve and statistics
     </description>
     <macros>
-        <import>vegan_macros.xml</import>
+        <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
@@ -127,11 +127,11 @@
     </tests>
     <help>
         <![CDATA[
-        
+
         Gives the expected species richness in random subsamples of size sample from the community. The size of sample should be smaller than total community size, but the function will work for larger sample as well (with a warning) and return non-rarefied species richness (and standard error = 0). Rarefaction can be performed only with genuine counts of individuals. The function rarefy is based on Hurlbert’s (1971) formulation, and the standard errors on Heck et al. (1975).
-        
+
         Returns probabilities that species occur in a rarefied community of size sample.
-        
+
         Draws a rarefaction curve for each row of the input data. The rarefaction curves are evaluated using the interval of step sample sizes, always including 1 and total sample size. If sample is specified, a vertical line is drawn at sample with horizontal lines for the rarefied species richnesses.
 
 
@@ -142,4 +142,4 @@
     </help>
     <citations>
     </citations>
-</tool>
\ No newline at end of file
+</tool>