Mercurial > repos > artbio > cpm_tpm_rpk
diff cpm_tpm_rpk.xml @ 7:f00c1c34565e draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk commit 8cca5f05212cd25113955fb9c11801f4047c12b4
| author | artbio |
|---|---|
| date | Wed, 03 Jul 2024 14:39:26 +0000 |
| parents | d2575928b824 |
| children |
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--- a/cpm_tpm_rpk.xml Sat Oct 14 16:24:48 2023 +0000 +++ b/cpm_tpm_rpk.xml Wed Jul 03 14:39:26 2024 +0000 @@ -1,10 +1,10 @@ -<tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.5.2"> +<tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPKM" version="0.6.0"> <description>from raw counts expression values</description> <requirements> - <requirement type="package" version="1.7.1">r-optparse</requirement> - <requirement type="package" version="0.16">r-rtsne</requirement> - <requirement type="package" version="3.3.6">r-ggplot2</requirement> - <requirement type="package" version="0.4.14">r-ggfortify</requirement> + <requirement type="package" version="1.7.5">r-optparse</requirement> + <requirement type="package" version="0.17">r-rtsne</requirement> + <requirement type="package" version="3.5.1">r-ggplot2</requirement> + <requirement type="package" version="0.4.17">r-ggfortify</requirement> <requirement type="package" version="1.4.4">r-reshape2</requirement> </requirements> <stdio> @@ -21,7 +21,7 @@ --gene_sep $option.gene_sep --gene_header $option.gene_header #end if - #if $option.type_transfo == "rpk": + #if $option.type_transfo == "rpkm": -f $option.gene_file --gene_sep $option.gene_sep --gene_header $option.gene_header @@ -64,7 +64,7 @@ <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> + <option value="rpkm">RPKM</option> <option value="none">NONE</option> </param> <when value="tpm"> @@ -82,7 +82,7 @@ <option value="FALSE">No</option> </param> </when> - <when value="rpk"> + <when value="rpkm"> <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> @@ -208,18 +208,18 @@ </test> <test expect_num_outputs="1"> <param name="input" value="counts.tab" ftype="tabular"/> - <param name="type_transfo" value="rpk"/> + <param name="type_transfo" value="rpkm"/> <param name="gene_file" value="gene_length.tab" ftype="tabular"/> <param name="gene_header" value="TRUE"/> - <output name="output" file="rpk.tab" ftype="tabular" /> + <output name="output" file="rpkm.tab" ftype="tabular" /> </test> <test expect_num_outputs="1"> <param name="input" value="counts.tab" ftype="tabular"/> - <param name="type_transfo" value="rpk"/> + <param name="type_transfo" value="rpkm"/> <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" /> + <output name="output" file="logrpkm.tab" ftype="tabular" /> </test> </tests> <help> @@ -231,7 +231,8 @@ 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). +- RPK (Reads Per Kilobase) are obtained by dividing read counts by gene lengths (expressed as kilo-nucleotides). +- RPKM (Reads Per Kilobase per Million of Counts) are obtained by dividing read counts by gene lengths (expressed in kilo-nucleotides) then by the sum of library counts (expressed as millions of reads) - 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.