Mercurial > repos > yqiancolumbia > ctk_test
comparison CITS.xml @ 0:0475e4175855 draft default tip
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
author | yqiancolumbia |
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date | Mon, 30 Apr 2018 05:25:11 -0400 |
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1 <tool id="CITS" name="CITS analysis"> | |
2 <description></description> | |
3 | |
4 <command interpreter="perl"> | |
5 /home/galaxy/tools/CTK/CITS.pl -v $bigFile -p $pvalue $multitest --gap $gap $uniqTagBed $uniqMutationTypeBed $output | |
6 </command> | |
7 | |
8 <inputs> | |
9 <param type="data" format="bed" name="uniqTagBed" label="Input file in BED format of unique tags"/> | |
10 <param type="data" format="bed" name="uniqMutationTypeBed" label="Input file in BED format of deletions, insertions, or substitutions corresponding to the tags above" /> | |
11 | |
12 <param name="bigFile" type="boolean" truevalue="-big" falsevalue="" checked="yes" label="This is a big file (over 6M lines)" /> | |
13 <param name="pvalue" type="float" value="0.001" label="Threshold of p-value of CITS" /> | |
14 <param name="multitest" type="boolean" truevalue="--multi-test" falsevalue="" checked="yes" label="Do Bonferroni multiple test correction" /> | |
15 <param name="gap" type="integer" value="25" label="Minimum gaps allowed between peaks (no merge cluster peaks if less than 0)" /> | |
16 </inputs> | |
17 | |
18 <outputs> | |
19 <data name="output" format="bed" label="CITS analysis on ${on_string}"/> | |
20 </outputs> | |
21 | |
22 <help> | |
23 | |
24 .. class:: warningmark | |
25 | |
26 Only certain variations of the CLIP protocol allow you to perform CITS analysis (e.g. iCLIP, BrdU CLIP, etc). | |
27 | |
28 ----- | |
29 | |
30 .. class:: infomark | |
31 | |
32 **What this tool does** | |
33 | |
34 Cross-linking induced trunction site (CITS) analysis | |
35 | |
36 Similar to CIMS analysis, This tool identifies clustered truncation sites and assigns statistical significance of the clustering based on a permutation based procedure. | |
37 | |
38 ----- | |
39 | |
40 Reference: | |
41 | |
42 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. | |
43 | |
44 </help> | |
45 </tool> |