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comparison ltr.xml @ 2:2fd354a78c56 draft

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author hyungrolee
date Sat, 14 Jun 2014 19:08:39 -0400
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1:b7ea9a0e2714 2:2fd354a78c56
1 <?xml version="1.0"?>
2
3 <tool name="MGEScan-LTR" id="mgescan-ltr" version="0.0.1" workflow_compatible="false">
4 <description>
5 de novo identification of LTR retroelements
6 </description>
7 <!--
8 <action module="galaxy.tools.actions.nonltr" class="nonltrToolAction"/>
9 <requirements>
10 <requirement type="package">HMMER</requirement>
11 <requirement type="package">EMBOSS</requirement>
12 </requirements>
13 -->
14 <command interpreter="bash">
15 <!--
16 /u/lee212/retrotminer/MGEScan_LTR/find_ltr.pl -genome=/u/lee212/retrotminer/MGEScan_nonLTR_v2/anoGam1/
17 -data=/u/lee212/retrotminer/MGEScan_LTR/example/data/ -program=/u/lee212/retrotminer/MGEScan_LTR/
18 -->
19 <!--mgescan.sh $input $input.name $hmmver $output L None None None $ltr_gff3 None-->
20 <!--mgescan.sh $input $input.name 3 $output L None None None $ltr_gff3 None-->
21 mgescan.sh $input $input.name 3 $output L None None None $ltr_gff3 None $sw_rm "$scaffold" $min_dist $max_dist $min_len_ltr $max_len_ltr $ltr_sim_condition $cluster_sim_condition $len_condition $repeatmasker
22 </command>
23 <inputs>
24 <!--
25 <param name="genome" type="text" label="directory where input genome data exists" />
26 <param name="data" type="text" label="directory of the output" />
27 -->
28 <param format="txt" name="input" type="data" label="From"/>
29 <!--param name="hmmver" type="select" label="Hmmsearch version">
30 <option selected="selected" value="3">3</option>
31 <option value="2">2</option>
32 </param-->
33 <!-- path.conf -->
34 <param name="sw_rm" type="select" display="checkboxes" multiple="True" label="enable repeatmasker, if necessary" help="Use this option if you are enable repeatmasker">
35 <option value="Yes">Yes</option>
36 </param>
37 <param name="scaffold" type="text" label="path for the big file that has all scaffolds"/>
38 <!-- value.conf -->
39 <param name="min_dist" type="text" value="2000" label="minimum distance(bp) between LTRs" />
40 <param name="max_dist" type="text" value="20000" label="maximum distance(bp) between LTRs" />
41 <param name="min_len_ltr" type="text" value="130" label="minimum length(bp) of LTR"/>
42 <param name="max_len_ltr" type="text" value="2000" label="maximum length(bp) of LTR"/>
43 <param name="ltr_sim_condition" type="text" value="70" label="minimum similarity(%) for LTRs in an element"/>
44 <param name="cluster_sim_condition" type="text" value="70" label="inimum similarity(%) for LTRs in a cluster"/>
45 <param name="len_condition" type="text" value="70" label="minimum length(bp) for LTRs aligned in local alignment"/>
46 </inputs>
47 <outputs>
48 <data format="ltr.out" name="output" />
49 <data format="gff3" name="ltr_gff3" />
50 <data format="repeatmasker" name="repeatmasker" >
51 <filter>sw_rm == "Yes"</filter>
52 </data>
53 </outputs>
54 <help>
55 Running the program
56 ===================
57
58 To run MGEScan-LTR, follow the steps below,
59
60 1. Specify options that you like to have:
61
62 * Check repeatmasker if you want to preprocess
63 * Check scaffold if the input file has all scaffolds.
64
65 2. Update values:
66
67 * min_dist: minimum distance(bp) between LTRs.
68 * max_dist: maximum distance(bp) between LTRS
69 * min_len_ltr: minimum length(bp) of LTR.
70 * max_len_ltr: maximum length(bp) of LTR.
71 * ltr_sim_condition: minimum similarity(%) for LTRs in an element.
72 * cluster_sim_condition: minimum similarity(%) for LTRs in a cluster
73 * len_condition: minimum length(bp) for LTRs aligned in local alignment.
74
75 4. Click 'Execute'
76
77 * mask known repeats other than LTR retrotransposons
78 * identify LTRs
79
80 Output
81 ======
82
83 Upon completion, MGEScan-LTR generates a file ltr.out. This output file has information
84 about clusters and coordinates of LTR retrotransposons identified. Each cluster of LTR
85 retrotransposons starts with the head line of [cluster_number]---------, followed by
86 the information of LTR retrotransposons in the cluster. The columns for LTR
87 retrotransposons are as follows.
88
89 1. LTR_id: unique id of LTRs identified. It consist of two components, sequence file name and id in the file. For example, chr1_2 is the second LTR retrotransposon in the chr1 file.
90 2. start position of 5 LTR.
91 3. end position of 5 LTR.
92 4. start position of 3 LTR.
93 5. end position of 3 LTR.
94 6. strand: + or -.
95 7. length of 5 LTR.
96 8. length of 3 LTR.
97 9. length of the LTR retrotransposon.
98 10. TSD on the left side of the LTR retotransposons.
99 11. TSD on the right side of the LTR retrotransposons.
100 12. di(tri)nucleotide on the left side of 5LTR
101 13. di(tri)nucleotide on the right side of 5LTR
102 14. di(tri)nucleotide on the left side of 3LTR
103 15. di(tri)nucleotide on the right side of 3LTR
104
105 License
106 ============
107
108 Copyright 2014 Mina Rho, Haixu Tang.
109 You may redistribute this software under the terms of the GNU General Public License.
110 </help>
111 </tool>