Mercurial > repos > iuc > ampvis2_alpha_diversity
comparison alpha_diversity.xml @ 8:77000428c613 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5
| author | iuc |
|---|---|
| date | Fri, 01 Nov 2024 17:09:34 +0000 |
| parents | 289d6299bd2e |
| children |
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| 7:c14c7fd4d1be | 8:77000428c613 |
|---|---|
| 1 <tool id="ampvis2_alpha_diversity" name="ampvis2 alpha diversity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> | 1 <tool id="ampvis2_alpha_diversity" name="ampvis2 alpha diversity" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT"> |
| 2 <description></description> | 2 <description></description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="header"/> | 6 <expand macro="header"/> |
| 9 ]]></command> | 9 ]]></command> |
| 10 <configfiles> | 10 <configfiles> |
| 11 <configfile name="rscript"><![CDATA[ | 11 <configfile name="rscript"><![CDATA[ |
| 12 #set m='"' + '", "'.join(str($measure).split(",")) + '"' | 12 #set m='"' + '", "'.join(str($measure).split(",")) + '"' |
| 13 library(ampvis2, quietly = TRUE) | 13 library(ampvis2, quietly = TRUE) |
| 14 | |
| 14 d <- readRDS("$data") | 15 d <- readRDS("$data") |
| 15 a <- amp_alphadiv(d, | 16 table <- amp_alphadiv(d, |
| 16 measure = c($m), | 17 measure = c($m), |
| 17 richness = $richness | 18 richness = $richness |
| 18 @RAREFY_TOKEN@ | 19 @RAREFY_TOKEN@, |
| 19 ) | 20 ) |
| 20 write.table(a, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE) | 21 plot <- amp_alphadiv(d, |
| 22 measure = c($m), | |
| 23 richness = $richness | |
| 24 @RAREFY_TOKEN@, | |
| 25 plot = TRUE, | |
| 26 plot_group_by = "$group_by", | |
| 27 plot_scatter = $plot_scatter | |
| 28 ) | |
| 29 write.table(table, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE) | |
| 30 ggsave("$alphadiv_plot", | |
| 31 plot = plot, | |
| 32 device = "$output_options.out_format" | |
| 33 #if str($output_options.plot_width) != '' | |
| 34 , width = $output_options.plot_width | |
| 35 #end if | |
| 36 #if str($output_options.plot_height) != '' | |
| 37 , height = $output_options.plot_height | |
| 38 #end if | |
| 39 ) | |
| 21 ]]></configfile> | 40 ]]></configfile> |
| 22 </configfiles> | 41 </configfiles> |
| 23 <inputs> | 42 <inputs> |
| 24 <expand macro="rds_input_macro"/> | 43 <expand macro="rds_input_macro"/> |
| 25 <param argument="measure" type="select" multiple="true" optional="false" label="Alpha-diversity measure(s) to be included"> | 44 <param argument="measure" type="select" multiple="true" optional="false" label="Alpha-diversity measure(s) to be included"> |
| 28 <option value="simpson" selected="true">simpson</option> | 47 <option value="simpson" selected="true">simpson</option> |
| 29 <option value="invsimpson" selected="true">invsimpson</option> | 48 <option value="invsimpson" selected="true">invsimpson</option> |
| 30 </param> | 49 </param> |
| 31 <param argument="richness" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Calculate sample richness estimates" help="Chao1 and ACE"/> | 50 <param argument="richness" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Calculate sample richness estimates" help="Chao1 and ACE"/> |
| 32 <expand macro="rarefy_macro" help="before calculating alpha diversity and/or richnes"/> | 51 <expand macro="rarefy_macro" help="before calculating alpha diversity and/or richnes"/> |
| 52 <param argument="group_by" type="text" label="Group by metadata field (for plotting)" help="Specify the metadata field to group the plot by"/> | |
| 53 <param argument="plot_scatter" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Scatter plot instead of boxplot?" help="Select to generate a scatter plot instead of a boxplot"/> | |
| 54 <expand macro="out_format_macro"/> | |
| 33 </inputs> | 55 </inputs> |
| 34 <outputs> | 56 <outputs> |
| 35 <data name="alphadiv" format="tabular"/> | 57 <data name="alphadiv" format="tabular"/> |
| 58 <expand macro="out_macro" name="alphadiv_plot" label=": plot"/> | |
| 36 </outputs> | 59 </outputs> |
| 37 <tests> | 60 <tests> |
| 38 <test> | 61 <test> |
| 39 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | 62 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> |
| 63 <param name="group_by" value="Plant"/> | |
| 64 <param name="plot_scatter" value="false"/> | |
| 40 <output name="alphadiv"> | 65 <output name="alphadiv"> |
| 41 <assert_contents> | 66 <assert_contents> |
| 42 <has_line line="SampleID	Plant	Date	Year	Period	Reads	uniqueOTUs	Shannon	Simpson	invSimpson"/> | 67 <has_line line="SampleID	Plant	Date	Year	Period	Reads	uniqueOTUs	Shannon	Simpson	invSimpson"/> |
| 43 <has_text text="16SAMP-536	"/> | 68 <has_text text="16SAMP-536	"/> |
| 44 <has_text text="	Aalborg West	"/> | 69 <has_text text="	Aalborg West	"/> |
| 45 <has_n_lines n="68"/> | 70 <has_n_lines n="68"/> |
| 46 <has_n_columns n="10"/> | 71 <has_n_columns n="10"/> |
| 47 </assert_contents> | 72 </assert_contents> |
| 48 </output> | 73 </output> |
| 74 <output name="alphadiv_plot" ftype="pdf"> | |
| 75 <assert_contents> | |
| 76 <has_size min="1"/> | |
| 77 </assert_contents> | |
| 78 </output> | |
| 49 </test> | 79 </test> |
| 50 <test> | 80 <test> |
| 51 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | 81 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> |
| 52 <param name="measure" value="observed,shannon"/> | 82 <param name="measure" value="observed,shannon"/> |
| 53 <param name="richness" value="true"/> | 83 <param name="richness" value="true"/> |
| 54 <param name="rarefy" value="500"/> | 84 <param name="rarefy" value="500"/> |
| 85 <param name="group_by" value="Plant"/> | |
| 86 <param name="plot_scatter" value="true"/> | |
| 55 <output name="alphadiv"> | 87 <output name="alphadiv"> |
| 56 <assert_contents> | 88 <assert_contents> |
| 57 <has_line line="SampleID	Plant	Date	Year	Period	RawReads	Reads	uniqueOTUs	Shannon	Simpson	invSimpson	Chao1	ACE"/> | 89 <has_line line="SampleID	Plant	Date	Year	Period	RawReads	Reads	uniqueOTUs	Shannon	Simpson	invSimpson	Chao1	ACE"/> |
| 58 <has_text text="16SAMP-536	"/> | 90 <has_text text="16SAMP-536	"/> |
| 59 <has_text text="	Aalborg West	"/> | 91 <has_text text="	Aalborg West	"/> |
| 60 <has_n_lines n="68"/> | 92 <has_n_lines n="68"/> |
| 61 <has_n_columns n="13"/> | 93 <has_n_columns n="13"/> |
| 62 <has_text text="	500	"/> | 94 <has_text text="	500	"/> |
| 95 </assert_contents> | |
| 96 </output> | |
| 97 <output name="alphadiv_plot"> | |
| 98 <assert_contents> | |
| 99 <has_size min="1"/> | |
| 63 </assert_contents> | 100 </assert_contents> |
| 64 </output> | 101 </output> |
| 65 </test> | 102 </test> |
| 66 </tests> | 103 </tests> |
| 67 <help><![CDATA[ | 104 <help><![CDATA[ |