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"planemo upload for repository https://github.com/McIntyre-Lab/BayesASE/tree/main/galaxy commit 9b70598ef46a73632d9e0fa0c6ce6776fb5e9d6a"
author | malex |
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date | Thu, 14 Jan 2021 21:51:36 +0000 |
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<tool id="base_reformat_design_file" name="Reformat Sample Design File" version="21.1.13"> <description>for use in Calculate Priors Module for BayesASE</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command> <![CDATA[ awk 'BEGIN{FS="\t"; OFS="\t"} { print $1"\t"$2"\t"$4}' ${DESIGN} | sort -u > ${OUTFILE} ]]> </command> <inputs> <param name="DESIGN" format="tabular,tsv" type="data" label="Input Sample Design file" help=" See help section for required format. The Sample Design file can be created using the Combine ASE Count Tables tool" /> </inputs> <outputs> <data name="OUTFILE" format="tabular" label="${tool.name} on ${on_string}: Prior Design File"/> </outputs> <tests> <test> <param name="DESIGN" value="BASE_testdata/summarize_counts_testdata/sample_df_BASE.tabular" ftype="tabular"/> <output name="OUTFILE" file="BASE_testdata/summarize_counts_testdata/prior_design_file.tsv" ftype="tsv"/> </test> </tests> <help><![CDATA[ **Tool Description** The Reformat Sample Design File tool takes the "Sample Design File” and modifies it to create the Priors Design File --------------------------------------------------------------------------------------------------------------------------- **Inputs** **Sample Design File** The input for this tool is the Sample Design File The Sample Design File can be created using the *Combine Counts Tables* tool. **The Sample Design File should contain the following columns, in order:** (1) G1 - name of updated parental genome 1 (2) G2 - name of updated parental genome 2 (3) sampleID - sample identifier (no spaces in name). Consists of a combination of comparate + replicate number (4) comparate- contains comparate information for testing allelic imbalance The comparate conditions must be written in the following format: {Genotype}_{condition} (ie W1118_V) Example of input Sample design file:: +-------+------+---------+----------+ | G1 | G2 |sampleID |comparate | +-------+------+---------+--------- + | W1118 | W55 | W55_M_1 | W55_M | +-------+------+---------+----------+ | W1118 | W55 | W55_M_2 | W55_M | +-------+------+---------+----------+ | W1118 | W55 | W55_M_3 | W55_M | +-------+------+---------+----------+ | W1118 | W55 | W55_V_1 | W55_V | +-------+------+---------+----------+ **Outputs** (1) A Priors Design File in TSV format with the sampleID column removed and the resulting file uniqued. Example of Priors Design File:: +-------+------+----------+ | G1 | G2 |comparate | +-------+------+----------+ | W1118 | W55 | W55_M | +-------+------+----------+ | W1118 | W55 | W55_M | +-------+------+----------+ | W1118 | W55 | W55_M | +-------+------+----------+ | W1118 | W55 | W55_V | +-------+------+----------+ ]]></help> <citations> <citation type="bibtex">@ARTICLE{Miller20BASE, author = {Brecca Miller, Alison Morse, Elyse Borgert, Gavin Gamble, Fei Zhou, Jeremy Newman, Fabio Marroni, Lauren M. McIntyre}, title = {BASE: Bayesian analysis of allele specific expression reveals statistically significant regulatory variation}, journal = {????}, year = {in press} }</citation> </citations> </tool>