Mercurial > repos > morinlab > generate_pyclone_input
changeset 0:6882251af034 draft
Uploaded
| author | morinlab |
|---|---|
| date | Sun, 04 Dec 2016 17:49:22 -0500 |
| parents | |
| children | 6702aeb5266a |
| files | generate_pyclone_input.xml |
| diffstat | 1 files changed, 49 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_pyclone_input.xml Sun Dec 04 17:49:22 2016 -0500 @@ -0,0 +1,49 @@ +<tool id="generate_pyclone_input" name="Generate PyClone input" version="14.2"> + <description> + Generate PyClone input files from SNV and copy number data + </description> + + <requirements> + <requirement type="package" version="1.0">generate_pyclone_input</requirement> + <requirement type="package" version="14.2">morinlab_scripts</requirement> + <requirement type="set_environment">MORINLAB_SCRIPTS</requirement> + </requirements> + + <stdio> + <exit_code range="1:" level="warning" /> + <exit_code range=":-1" level="warning" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + + <command> + Rscript \$MORINLAB_SCRIPTS/generate_pyclone_input/generate_pyclone_input.R + $segments $segments_mode $maf $sample_id .; + + mv ./${sample_id}_pyclone_in.tsv $pyclone_input; + </command> + + <inputs> + <!-- Required inputs --> + <param type="data" name="segments" format="tabular" label="Sequenza, Titan, OncoSNP, or IGV-friendly segments file"/> + <param name="segments_mode" label="Specify the source of the segments file" type="select"> + <option value="S">Sequenza</option> + <option value="T">Titan</option> + <option value="I">IGV-friendly</option> + </param> + <param type="data" name="maf" format="tabular" label="Patient MAF file"/> + <param type="text" name="sample_id" size="20" label="Sample ID"/> + </inputs> + + <outputs> + <data format="tabular" name="pyclone_input"/> + </outputs> + + <tests> + </tests> + + <help> + </help> + +</tool> +