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author | yqiancolumbia |
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date | Mon, 30 Apr 2018 05:25:11 -0400 |
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<tool id="T2C" name="Get the distribution of the different substitutions"> <description></description> <command interpreter="python"> /home/galaxy/tools/CTK/T2C.py $input $output_T2Cfiltered $output_substitutions $output_frequencies </command> <inputs> <param name="input" type="data" format="tabular" label="Input unique mutation file of PAR-CLIP 4SU in tabular format"/> </inputs> <outputs> <data name="output_T2Cfiltered" format="tabular" label="Tag_uniq_T2C file on ${on_string}" /> <data name="output_substitutions" format="tabular" label="Tag_uniq_sub file on ${on_string}" /> <data name="output_frequencies" format="tabular" label="Tag_uniq_freq file on ${on_string}" /> </outputs> <help> .. class:: infomark **What this tool does** It may be useful to get the distribution of the different substitutions that are prevalent. The reason for this is because PAR-CLIP 4SU is known for inducing substitutions (more so than deletions and insertions), specifically by inducing a T to C transition on the forward strand (same as A to G on negative strand). There are three output files, one of which will be used in the CIMS analysis moving forward. ----- **Output** (1) T2Cfiltered file = filtered to only contain T to C substitutions, which we will use in CIMS analysis downstream (2) substitutions file = filtered to only contain ALL substitutions (as opposed to all mutations) (3) frequencies file = contains a summary of the frequency of all substitutions Confirm that most of the substitutions are in fact T to C by looking at the frequency column in the frequencies file. </help> </tool>