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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122 |
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modified:
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 |
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| diff -r 3d1d965b6423 -r dd2705a31239 test-data/vegan_output_richness.tabular --- 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 |
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| @@ -1,2 +1,2 @@ -"" "x" -"V2" 22 + x +V2 22 |
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| diff -r 3d1d965b6423 -r dd2705a31239 test-data/vegan_output_slope.tabular --- 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 |
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| @@ -1,2 +1,2 @@ -"x" -"V2" 0.000807519626095124 +x +V2 0.000807519626095124 |
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| diff -r 3d1d965b6423 -r dd2705a31239 test-data/vegan_output_species_count.tabular --- 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 |
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| @@ -1,2 +1,2 @@ -"" "x" -"V2" 22 + x +V2 22 |
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| diff -r 3d1d965b6423 -r dd2705a31239 test-data/vegan_output_species_frequency.tabular --- 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 |
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| @@ -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 |
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| diff -r 3d1d965b6423 -r dd2705a31239 test-data/vegan_output_species_probabilities.tabular --- 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 |
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| @@ -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 |
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| diff -r 3d1d965b6423 -r dd2705a31239 vegan_rarefaction.xml --- a/vegan_rarefaction.xml Wed Dec 23 13:55:57 2015 -0500 +++ b/vegan_rarefaction.xml Mon Feb 08 15:24:42 2016 -0500 |
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| @@ -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> |