Mercurial > repos > yqiancolumbia > ctk_test
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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="CITS" name="CITS analysis"> <description></description> <command interpreter="perl"> /home/galaxy/tools/CTK/CITS.pl -v $bigFile -p $pvalue $multitest --gap $gap $uniqTagBed $uniqMutationTypeBed $output </command> <inputs> <param type="data" format="bed" name="uniqTagBed" label="Input file in BED format of unique tags"/> <param type="data" format="bed" name="uniqMutationTypeBed" label="Input file in BED format of deletions, insertions, or substitutions corresponding to the tags above" /> <param name="bigFile" type="boolean" truevalue="-big" falsevalue="" checked="yes" label="This is a big file (over 6M lines)" /> <param name="pvalue" type="float" value="0.001" label="Threshold of p-value of CITS" /> <param name="multitest" type="boolean" truevalue="--multi-test" falsevalue="" checked="yes" label="Do Bonferroni multiple test correction" /> <param name="gap" type="integer" value="25" label="Minimum gaps allowed between peaks (no merge cluster peaks if less than 0)" /> </inputs> <outputs> <data name="output" format="bed" label="CITS analysis on ${on_string}"/> </outputs> <help> .. class:: warningmark Only certain variations of the CLIP protocol allow you to perform CITS analysis (e.g. iCLIP, BrdU CLIP, etc). ----- .. class:: infomark **What this tool does** Cross-linking induced trunction site (CITS) analysis Similar to CIMS analysis, This tool identifies clustered truncation sites and assigns statistical significance of the clustering based on a permutation based procedure. ----- Reference: Weyn-Vanhentenryck,S.,M.*, Mele,A.*, Yan,Q.*, Sun,S., Farny,N., Zhang,Z., Xue,C., Herre,M., Silver,P.A., Zhang,M.Q., Krainer,A.R., Darnell,R.B. †, Zhang,C. † 2014. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep. 10.1016/j.celrep.2014.02.005. </help> </tool>