| Previous changeset 2:db56c8e79b1e (2016-11-07) Next changeset 4:a1b80a746054 (2024-03-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7 |
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modified:
vegan_diversity.xml |
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added:
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 |
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removed:
tool_dependencies.xml vegan_macros.xml |
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| diff -r db56c8e79b1e -r a2c047a2c380 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Sep 07 11:30:36 2018 -0400 |
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| @@ -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> |
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| diff -r db56c8e79b1e -r a2c047a2c380 test-data/output_fisher_alpha.tabular --- /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 |
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| @@ -0,0 +1,2 @@ + x +V2 2.86498950425242 |
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| diff -r db56c8e79b1e -r a2c047a2c380 test-data/vegan_output_richness.tabular --- /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 |
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| @@ -0,0 +1,2 @@ + x +V2 22 |
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| diff -r db56c8e79b1e -r a2c047a2c380 test-data/vegan_output_slope.tabular --- /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 |
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| @@ -0,0 +1,2 @@ +x +V2 0.000807519626095124 |
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| diff -r db56c8e79b1e -r a2c047a2c380 test-data/vegan_output_species_count.tabular --- /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 |
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| @@ -0,0 +1,2 @@ + x +V2 22 |
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| diff -r db56c8e79b1e -r a2c047a2c380 test-data/vegan_output_species_frequency.tabular --- /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 |
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| @@ -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 |
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| diff -r db56c8e79b1e -r a2c047a2c380 test-data/vegan_output_species_probabilities.tabular --- /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 |
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| @@ -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 |
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| diff -r db56c8e79b1e -r a2c047a2c380 tool_dependencies.xml --- a/tool_dependencies.xml Mon Nov 07 17:43:22 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |
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| diff -r db56c8e79b1e -r a2c047a2c380 vegan_diversity.xml --- a/vegan_diversity.xml Mon Nov 07 17:43:22 2016 -0500 +++ b/vegan_diversity.xml Fri Sep 07 11:30:36 2018 -0400 |
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| @@ -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> |
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| diff -r db56c8e79b1e -r a2c047a2c380 vegan_macros.xml --- a/vegan_macros.xml Mon Nov 07 17:43:22 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |