diff CITS.xml @ 0:0475e4175855 draft default tip

planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CITS.xml	Mon Apr 30 05:25:11 2018 -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>