Mercurial > repos > iuc > vegan_rarefaction

changeset 1:dd2705a31239 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
author iuc
date Mon, 08 Feb 2016 15:24:42 -0500
parents 3d1d965b6423
children b0d5976540e3
files 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 vegan_rarefaction.xml
diffstat 6 files changed, 70 insertions(+), 62 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/vegan_output_richness.tabular	Wed Dec 23 13:55:57 2015 -0500
+++ b/test-data/vegan_output_richness.tabular	Mon Feb 08 15:24:42 2016 -0500
@@ -1,2 +1,2 @@
-""	"x"
-"V2"	22
+	x
+V2	22
--- a/test-data/vegan_output_slope.tabular	Wed Dec 23 13:55:57 2015 -0500
+++ b/test-data/vegan_output_slope.tabular	Mon Feb 08 15:24:42 2016 -0500
@@ -1,2 +1,2 @@
-"x"
-"V2"	0.000807519626095124
+x
+V2	0.000807519626095124
--- a/test-data/vegan_output_species_count.tabular	Wed Dec 23 13:55:57 2015 -0500
+++ b/test-data/vegan_output_species_count.tabular	Mon Feb 08 15:24:42 2016 -0500
@@ -1,2 +1,2 @@
-""	"x"
-"V2"	22
+	x
+V2	22
--- a/test-data/vegan_output_species_frequency.tabular	Wed Dec 23 13:55:57 2015 -0500
+++ b/test-data/vegan_output_species_frequency.tabular	Mon Feb 08 15:24:42 2016 -0500
@@ -1,23 +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
+	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
--- a/test-data/vegan_output_species_probabilities.tabular	Wed Dec 23 13:55:57 2015 -0500
+++ b/test-data/vegan_output_species_probabilities.tabular	Mon Feb 08 15:24:42 2016 -0500
@@ -1,23 +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
+	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/vegan_rarefaction.xml	Wed Dec 23 13:55:57 2015 -0500
+++ b/vegan_rarefaction.xml	Mon Feb 08 15:24:42 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="vegan_rarefaction" name="Vegan Rarefaction" version="0.0.2">
+<tool id="vegan_rarefaction" name="Vegan Rarefaction" version="0.0.3">
     <description>
         curve and statistics
     </description>
@@ -32,24 +32,28 @@
 sprintf("Using sample size: %i", raremax)
 Srare <- rarefy(input_abundance, sample=raremax, se=FALSE, MARGIN=1)
 #if "output_richness" in $include_files:
-write.table(Srare, "${output_richness}", col.names=NA, sep = "\t")
+write.table(Srare, "${output_richness}", quote=FALSE, col.names=NA, sep = "\t")
 #end if
 
 #if "output_slope" in $include_files:
-write.table(rareslope(input_abundance, sample=raremax+raremax_offset), "${output_slope}", sep = "\t")
+write.table(rareslope(input_abundance, sample=raremax+raremax_offset), "${output_slope}", quote=FALSE, sep = "\t")
 #end if
 
 S <- specnumber(input_abundance)
 #if "output_species_count" in $include_files:
-write.table(S, "${ output_species_count }", col.names=NA, sep="\t" )
+write.table(S, "${ output_species_count }", quote=FALSE, col.names=NA, sep="\t" )
 #end if
 
 #if "output_species_frequency" in $include_files:
-write.table(specnumber(input_abundance, MARGIN=2), "${ output_species_frequency }", col.names=NA, sep="\t" )
+write.table(specnumber(input_abundance, MARGIN=2), "${ output_species_frequency }", quote=FALSE, col.names=NA, sep="\t" )
 #end if
 
 #if "output_species_probabilities" in $include_files:
-write.table(drarefy(input_abundance, sample=raremax+raremax_offset), "${ output_species_probabilities }", col.names=NA, sep="\t" )
+write.table(drarefy(input_abundance, sample=raremax+raremax_offset), "${ output_species_probabilities }", quote=FALSE, col.names=NA, sep="\t" )
+#end if
+
+#if "output_random_rarefied" in $include_files:
+write.table( t( rrarefy(input_abundance, sample=raremax) ), "${ output_random_rarefied }", quote=FALSE, col.names=NA, sep="\t" )
 #end if
 
 #if "output_plot" in $include_files:
@@ -73,8 +77,9 @@
             <option value="output_richness" selected="true">Richness</option>
             <option value="output_species_probabilities" selected="true">Species probabilities</option>
             <option value="output_slope" selected="true">Slope of rarefaction curve</option>
+            <option value="output_plot" selected="true">Rarefaction plot</option>
+            <option value="output_random_rarefied" selected="true">Randomly rarefied community matrix</option>
             <option value="output_r_script" selected="false">R script</option>
-            <option value="output_plot" selected="true">Rarefaction plot</option>
         </param>
     </inputs>
     <outputs>
@@ -93,12 +98,15 @@
         <data format="tabular" name="output_slope" label="${tool.name} on ${on_string} (slope of curve)">
             <filter>"output_slope" in include_outputs</filter>
         </data>
+        <data format="png" name="output_plot" label="${tool.name} on ${on_string} (plot)">
+            <filter>"output_plot" in include_outputs</filter>
+        </data>
+        <data format="tabular" name="output_random_rarefied" label="${tool.name} on ${on_string} (Random rarefied community matrix)">
+            <filter>"output_random_rarefied" in include_outputs</filter>
+        </data>
         <data format="txt" name="output_r_script" label="${tool.name} on ${on_string} (Rscript)">
             <filter>"output_r_script" in include_outputs</filter>
         </data>
-        <data format="png" name="output_plot" label="${tool.name} on ${on_string} (plot)">
-            <filter>"output_plot" in include_outputs</filter>
-        </data>
     </outputs>
     <tests>
         <test>