Mercurial > repos > artbio > cpm_tpm_rpk
diff cpm_tpm_rpk.xml @ 0:35d032c46a4e draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
| author | artbio |
|---|---|
| date | Wed, 25 Jul 2018 13:05:17 -0400 |
| parents | |
| children | b74bab5157c4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpm_tpm_rpk.xml Wed Jul 25 13:05:17 2018 -0400 @@ -0,0 +1,161 @@ +<tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.1.0"> + <description>from raw counts expression values</description> + <requirements> + <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</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 +]]></command> + <inputs> + <param name="input" type="data" format="txt" label="Raw counts of expression data"/> + <param name="input_sep" type="select" label="Input column separator"> + <option value="tab" selected="true">Tabs</option> + <option value=",">Comma</option> + <option value="\ ">Whitespace</option> + <option value=".">Dots</option> + <option value="_">Underscores</option> + <option value="-">Dashes</option> + </param> + <param name="input_header" type="select" label="Consider first line of input file as header?"> + <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> + </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> + </inputs> + <outputs> + <data name="output" format="tabular" label="${option.type_transfo} from ${on_string}"> + <filter>log == "FALSE"</filter> + </data> + <data name="output_log" format="tabular" label="log2(${option.type_transfo} +1) from ${on_string}"> + <filter>log == "TRUE"</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <param name="type_transfo" value="cpm"/> + <output name="output" file="cpm.tab" ftype="tabular"/> + </test> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <param name="type_transfo" value="cpm"/> + <param name="log" value="TRUE"/> + <output name="output" file="logcpm.tab" ftype="tabular"/> + </test> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <param name="type_transfo" value="tpm"/> + <param name="gene_file" value="gene_length.tab" ftype="tabular"/> + <param name="gene_header" value="TRUE"/> + <output name="output" file="tpm.tab" ftype="tabular"/> + </test> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <param name="type_transfo" value="tpm"/> + <param name="gene_file" value="gene_length.tab" ftype="tabular"/> + <param name="gene_header" value="TRUE"/> + <param name="log" value="TRUE"/> + <output name="output" file="logtpm.tab" ftype="tabular"/> + </test> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <param name="type_transfo" value="rpk"/> + <param name="gene_file" value="gene_length.tab" ftype="tabular"/> + <param name="gene_header" value="TRUE"/> + <output name="output" file="rpk.tab" ftype="tabular"/> + </test> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <param name="type_transfo" value="rpk"/> + <param name="gene_file" value="gene_length.tab" ftype="tabular"/> + <param name="gene_header" value="TRUE"/> + <param name="log" value="TRUE"/> + <output name="output" file="logrpk.tab" ftype="tabular"/> + </test> + </tests> + <help> + +**What it does** + +And returns a table of normalized expression values. + +Normalization can be: + +- CPM (Counts Per Million) are obtained by dividing counts by the library counts sum and multiplying the results by a million. +- RPK (Reads Per Kilobases) are obtained by dividing read counts by gene lengths (expressed in kilo-nucleotides). +- TPM (Transcripts Per Million) are obtained by dividing RPK values by the sum of all RPK values in a sample and multiplying the results by 1 million. + +RPK and TPM require a two-column correspondance table gene_name - gene length where the length is specified in nucleotide. Both these metrics are relevant only for sequencing of full length RNAs. + +Note: do not comment you header line if you have header line in you tabular input (ie do not start the header line with a '#' character) + +Computed values may be log-transformed (log2([CPM or RPK or TPM]+1)) + + </help> +</tool>