Mercurial > repos > artbio > cpm_tpm_rpk
diff cpm_tpm_rpk.xml @ 1:b74bab5157c4 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
| author | artbio |
|---|---|
| date | Tue, 05 Feb 2019 19:51:38 -0500 |
| parents | 35d032c46a4e |
| children | 563337e780ce |
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--- a/cpm_tpm_rpk.xml Wed Jul 25 13:05:17 2018 -0400 +++ b/cpm_tpm_rpk.xml Tue Feb 05 19:51:38 2019 -0500 @@ -1,34 +1,42 @@ -<tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.1.0"> +<tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.2.0"> <description>from raw counts expression values</description> <requirements> <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> + <requirement type="package" version="0.13=r3.3.2_0">r-rtsne</requirement> + <requirement type="package" version="2.2.1=r3.3.2_0">r-ggplot2</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> <command detect_errors="exit_code"><![CDATA[ -Rscript $__tool_directory__/cpm_tpm_rpk.R --d $input --t $option.type_transfo --s $input_sep --c $input_header -#if $option.type_transfo == "tpm": --f $option.gene_file ---gene_sep $option.gene_sep ---gene_header $option.gene_header -#end if -#if $option.type_transfo == "rpk": --f $option.gene_file ---gene_sep $option.gene_sep ---gene_header $option.gene_header -#end if --l $log -#if $log == "FALSE": --o ${output} -#end if -#if $log == "TRUE": --o ${output_log} -#end if + Rscript $__tool_directory__/cpm_tpm_rpk.R + -d $input + -t $option.type_transfo + -s $input_sep + -c $input_header + #if $option.type_transfo == "tpm": + -f $option.gene_file + --gene_sep $option.gene_sep + --gene_header $option.gene_header + #end if + #if $option.type_transfo == "rpk": + -f $option.gene_file + --gene_sep $option.gene_sep + --gene_header $option.gene_header + #end if + -l $log + #if $log == "FALSE": + -o ${output} + #else if $log == "TRUE": + -o ${output_log} + #end if + #if $visu_option.visualisation == "tsne": + --tsne 'TRUE' + --seed '$visu_option.seed' + --perp '$visu_option.perp' + --theta '$visu_option.theta' + --tsne_out '$tsne_out' + #end if ]]></command> <inputs> <param name="input" type="data" format="txt" label="Raw counts of expression data"/> @@ -44,49 +52,61 @@ <option value="TRUE" selected="true">Yes</option> <option value="FALSE">No</option> </param> - <conditional name="option"> - <param name="type_transfo" type="select" label="Type of transformation"> - <option value="cpm" selected="true">CPM</option> - <option value="tpm">TPM</option> - <option value="rpk">RPK</option> - </param> - <when value="tpm"> - <param name="gene_file" type="data" format="txt" label="Gene length file"/> - <param name="gene_sep" type="select" label="Gene length column separator"> - <option value="tab" selected="true">Tabs</option> - <option value=",">Commas</option> - <option value="\ ">Whitespaces</option> - <option value=".">Dots</option> - <option value="_">Underscores</option> - <option value="-">Dashes</option> - </param> - <param name="gene_header" type="select" label="Consider first line of gene length file as header ?"> - <option value="TRUE" selected="true">Yes</option> - <option value="FALSE">No</option> + <conditional name="option"> + <param name="type_transfo" type="select" label="Type of transformation"> + <option value="cpm" selected="true">CPM</option> + <option value="tpm">TPM</option> + <option value="rpk">RPK</option> </param> - </when> - <when value="rpk"> - <param name="gene_file" type="data" format="txt" label="Gene length file"/> - <param name="gene_sep" type="select" label="Gene length column separator"> - <option value="tab" selected="true">Tabs</option> - <option value=",">Commas</option> - <option value="\ ">Whitespaces</option> - <option value=".">Dots</option> - <option value="_">Underscores</option> - <option value="-">Dashes</option> - </param> - <param name="gene_header" type="select" label="Consider first line of gene length file as header ?"> - <option value="TRUE" selected="true">Yes</option> - <option value="FALSE">No</option> - </param> - </when> - <when value="cpm"> - </when> - </conditional> + <when value="tpm"> + <param name="gene_file" type="data" format="txt" label="Gene length file"/> + <param name="gene_sep" type="select" label="Gene length column separator"> + <option value="tab" selected="true">Tabs</option> + <option value=",">Commas</option> + <option value="\ ">Whitespaces</option> + <option value=".">Dots</option> + <option value="_">Underscores</option> + <option value="-">Dashes</option> + </param> + <param name="gene_header" type="select" label="Consider first line of gene length file as header ?"> + <option value="TRUE" selected="true">Yes</option> + <option value="FALSE">No</option> + </param> + </when> + <when value="rpk"> + <param name="gene_file" type="data" format="txt" label="Gene length file"/> + <param name="gene_sep" type="select" label="Gene length column separator"> + <option value="tab" selected="true">Tabs</option> + <option value=",">Commas</option> + <option value="\ ">Whitespaces</option> + <option value=".">Dots</option> + <option value="_">Underscores</option> + <option value="-">Dashes</option> + </param> + <param name="gene_header" type="select" label="Consider first line of gene length file as header ?"> + <option value="TRUE" selected="true">Yes</option> + <option value="FALSE">No</option> + </param> + </when> + <when value="cpm"> + </when> + </conditional> <param name="log" type="select" label="Data should be log transformed ?"> <option value="FALSE" selected="true">No</option> <option value="TRUE">Yes</option> </param> + <conditional name="visu_option"> + <param name="visualisation" type="select" label="Visualisation of data with various dimensionality reduction methods" > + <option value="no" selected="true">No visualisation</option> + <option value="tsne" >tsne</option> + </param> + <when value="tsne"> + <param name="seed" value="42.0" type="float" label="Seed value for reproducibiity" help="Set to 42 as default" /> + <param name="perp" value="10.0" type="float" label="perplexity"/> + <param name="theta" value="1.0" type="float" label="theta"/> + </when> + <when value="no" /> + </conditional> </inputs> <outputs> <data name="output" format="tabular" label="${option.type_transfo} from ${on_string}"> @@ -94,9 +114,24 @@ </data> <data name="output_log" format="tabular" label="log2(${option.type_transfo} +1) from ${on_string}"> <filter>log == "TRUE"</filter> - </data> + </data> + <data name="tsne_out" format="pdf" label="tsne from ${on_string}"> + <filter>visu_option['visualisation'] == 'tsne'</filter> + </data> </outputs> <tests> + <!-- test t-SNE --> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <param name="type_transfo" value="cpm"/> + <param name="visualisation" value="tsne"/> + <param name="seed" value="49"/> + <param name="perp" value="2"/> + <param name="theta" value="1" /> + <output name="output" file="cpm.tab" ftype="tabular"/> + <output name="tsne_out" file="tsne.pdf" ftype="pdf"/> + </test> + <!-- test without t-SNE --> <test> <param name="input" value="counts.tab" ftype="tabular"/> <param name="type_transfo" value="cpm"/> @@ -143,7 +178,7 @@ **What it does** -And returns a table of normalized expression values. +Takes a raw count expression matrix and returns a table of normalized expression values. Normalization can be: