diff T2C.xml @ 0:0475e4175855 draft default tip

planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/T2C.xml	Mon Apr 30 05:25:11 2018 -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>