Mercurial > repos > yqiancolumbia > ctk_test
comparison T2C.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="T2C" name="Get the distribution of the different substitutions"> | |
2 <description></description> | |
3 | |
4 <command interpreter="python"> | |
5 /home/galaxy/tools/CTK/T2C.py $input $output_T2Cfiltered $output_substitutions $output_frequencies | |
6 </command> | |
7 | |
8 <inputs> | |
9 <param name="input" type="data" format="tabular" label="Input unique mutation file of PAR-CLIP 4SU in tabular format"/> | |
10 </inputs> | |
11 | |
12 <outputs> | |
13 <data name="output_T2Cfiltered" format="tabular" label="Tag_uniq_T2C file on ${on_string}" /> | |
14 <data name="output_substitutions" format="tabular" label="Tag_uniq_sub file on ${on_string}" /> | |
15 <data name="output_frequencies" format="tabular" label="Tag_uniq_freq file on ${on_string}" /> | |
16 </outputs> | |
17 <help> | |
18 | |
19 .. class:: infomark | |
20 | |
21 **What this tool does** | |
22 | |
23 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). | |
24 There are three output files, one of which will be used in the CIMS analysis moving forward. | |
25 | |
26 ----- | |
27 | |
28 **Output** | |
29 | |
30 (1) T2Cfiltered file = filtered to only contain T to C substitutions, which we will use in CIMS analysis downstream | |
31 | |
32 (2) substitutions file = filtered to only contain ALL substitutions (as opposed to all mutations) | |
33 | |
34 (3) frequencies file = contains a summary of the frequency of all substitutions | |
35 | |
36 Confirm that most of the substitutions are in fact T to C by looking at the frequency column in the frequencies file. | |
37 | |
38 </help> | |
39 </tool> |