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