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changeset 3:a2c047a2c380 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
author iuc
date Fri, 07 Sep 2018 11:30:36 -0400
parents db56c8e79b1e
children a1b80a746054
files macros.xml test-data/output_fisher_alpha.tabular test-data/vegan_output_richness.tabular test-data/vegan_output_slope.tabular test-data/vegan_output_species_count.tabular test-data/vegan_output_species_frequency.tabular test-data/vegan_output_species_probabilities.tabular tool_dependencies.xml vegan_diversity.xml vegan_macros.xml
diffstat 10 files changed, 105 insertions(+), 63 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Sep 07 11:30:36 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_fisher_alpha.tabular	Fri Sep 07 11:30:36 2018 -0400
@@ -0,0 +1,2 @@
+	x
+V2	2.86498950425242
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vegan_output_richness.tabular	Fri Sep 07 11:30:36 2018 -0400
@@ -0,0 +1,2 @@
+	x
+V2	22
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vegan_output_slope.tabular	Fri Sep 07 11:30:36 2018 -0400
@@ -0,0 +1,2 @@
+x
+V2	0.000807519626095124
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vegan_output_species_count.tabular	Fri Sep 07 11:30:36 2018 -0400
@@ -0,0 +1,2 @@
+	x
+V2	22
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vegan_output_species_frequency.tabular	Fri Sep 07 11:30:36 2018 -0400
@@ -0,0 +1,23 @@
+	x
+        Bacteroidetes	1
+        Chlorobi	1
+      Firmicutes	1
+      Proteobacteria	1
+      Actinobacteria	1
+      Cyanobacteria	1
+        Acidobacteria	1
+        Fibrobacteres	1
+      Chloroflexi	1
+      Gemmatimonadetes	1
+      Aquificae	1
+      Tenericutes	1
+      Planctomycetes	1
+      Nitrospirae	1
+        Verrucomicrobia	1
+      Thermotogae	1
+      Fusobacteria	1
+      Deinococcus-Thermus	1
+      Elusimicrobia	1
+      Deferribacteres	1
+      Spirochaetes	1
+      Euryarchaeota	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vegan_output_species_probabilities.tabular	Fri Sep 07 11:30:36 2018 -0400
@@ -0,0 +1,23 @@
+	x
+        Bacteroidetes	1
+        Chlorobi	1
+      Firmicutes	1
+      Proteobacteria	1
+      Actinobacteria	1
+      Cyanobacteria	1
+        Acidobacteria	1
+        Fibrobacteres	1
+      Chloroflexi	1
+      Gemmatimonadetes	1
+      Aquificae	1
+      Tenericutes	1
+      Planctomycetes	1
+      Nitrospirae	1
+        Verrucomicrobia	1
+      Thermotogae	1
+      Fusobacteria	1
+      Deinococcus-Thermus	0.99983850129199
+      Elusimicrobia	0.99983850129199
+      Deferribacteres	0.99983850129199
+      Spirochaetes	0.99983850129199
+      Euryarchaeota	0.99983850129199
--- a/tool_dependencies.xml	Mon Nov 07 17:43:22 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="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
--- a/vegan_diversity.xml	Mon Nov 07 17:43:22 2016 -0500
+++ b/vegan_diversity.xml	Fri Sep 07 11:30:36 2018 -0400
@@ -1,9 +1,9 @@
-<tool id="vegan_diversity" name="Vegan Diversity" version="0.0.3">
+<tool id="vegan_diversity" name="Vegan Diversity" version="@TOOL_VERSION@">
     <description>
         index
     </description>
     <macros>
-        <import>vegan_macros.xml</import>
+        <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
@@ -64,7 +64,7 @@
             <param name="index_type_selector" value="shannon"/>
             <param name="margin" value="1"/>
             <param name="base" value="exp(1)"/>
-            <output name="output_slope" ftype="tabular" file="output_diversity_index.tabular" />
+            <output name="output_diversity_index" ftype="tabular" file="output_diversity_index.tabular" />
         </test>
     </tests>
     <help>
--- a/vegan_macros.xml	Mon Nov 07 17:43:22 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +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>
-            <!-- Conda dependency -->
-            <requirement type="package" version="2.3_0">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="@VERSION@">2.3-0</token>
-
-</macros>