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 |
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@@ -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 |
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@@ -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 |
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@@ -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> |