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comparison glimmer_extract.xml @ 0:e7c43934d083 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
author iuc
date Tue, 28 Nov 2017 09:54:34 -0500
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1 <tool id="glimmer_extract" name="Extract sequence regions" version="@WRAPPER_VERSION@">
2 <description>from a genome</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command><![CDATA[
8 extract
9 -t
10 '$seqInput'
11 '$cordInput' > '$output'
12 2> /dev/null
13 ]]></command>
14 <inputs>
15 <param name="seqInput" type="data" format="fasta" label="Genome Sequence"/>
16 <param name="cordInput" type="data" format="tabular" label="Coordinates" help="See Help below"/>
17 </inputs>
18 <outputs>
19 <data format="fasta" name="output" />
20 </outputs>
21 <tests>
22 <test>
23 <param name="seqInput" value='streptomyces_Tu6071_genomic.fasta'/>
24 <param name="cordInput" value='coordTest.txt'/>
25 <output name="output" file='extractTestOutput.fasta' compare="sim_size" delta="20"/>
26 </test>
27 </tests>
28
29 <help><![CDATA[
30
31 **What it does**
32
33 This program reads a genome sequence and a list of coordinates for it and outputs a multi-
34 fasta file of the regions specified by the coordinates.
35
36 -----
37
38 **Glimmer Overview**
39
40 ::
41
42 ************** ************** ************** **************
43 * * * * * * * *
44 * long-orfs * ===> * Extract * ===> * build-icm * ===> * glimmer3 *
45 * * * * * * * *
46 ************** ************** ************** **************
47
48 -----
49
50 **Example**
51
52
53 * input ::
54
55 -Genome Sequence
56
57 CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
58 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
59 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
60 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
61 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
62 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
63 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
64 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
65 CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
66 TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
67 AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
68 GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
69 AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
70 CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
71 AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
72 GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
73 ...
74
75 - Coorinates
76
77 00001 40137 52 +2 0.892
78 00002 1319 1095 -3 0.654
79 00003 1555 1391 -2 0.793
80 00004 1953 2066 +3 1.078
81 00005 2045 2146 +2 0.919
82 00006 4463 4759 +2 0.985
83 00007 6785 6582 -3 1.033
84 00008 6862 7020 +1 0.915
85 00009 7300 7488 +1 0.900
86 00010 7463 7570 +2 0.912
87 00011 8399 8527 +2 1.044
88 00012 10652 10545 -3 0.895
89 00013 12170 12066 -3 1.108
90 00014 13891 13748 -2 0.998
91 00015 14157 14044 -1 1.026
92 00016 15285 15410 +3 0.928
93 00017 15829 15704 -2 0.949
94 ...
95
96 * output::
97
98 >00001 40137 52 len=135
99 ATGACACATTTGCTCGTTGCTTTGACCCACTACGAGGCCAGTATCATGATTTCTAGAAAA
100 ACCCTCTTTTTGACTTCTTCCTCCATGATCCTTGTAGATTTTGAATTTGAAGTTTTTTCT
101 CATTCCAAAACTCTG
102
103 >00002 1319 1095 len=222
104 TTGGCTCGCCGTTTTGGAGTCCGTGCTGGAATGCCTGGCTTCATCTCAAATAAACTTTGT
105 CCGAGTCTAACGATTGTTCCAGGAAATTACCCTAAATACACTAAAGTCAGTCGCCAATTT
106 TCACAAATTTTCATGGAATACGATTCGGATGTTGGAATGATGTCATTGGATGAGGCATTT
107 ATAGATTTGACAGACTATGTGGCAAGTAATACAGAAAAAAGT
108
109 >00003 1555 1391 len=162
110 ATGGAGAATCTTGAGATGAAACTGGAATCATCTAGAGATTTATCAAGAGACTGTGTTTGT
111 ATAGATATGGATGCTTATTTTGCCGCAGTTGAAATGAGAGATAATCCTGCACTGAGAACA
112 GTTCCTATGGCCGTAGGCTCATCGGCAATGCTGGTAAGCACC
113
114 >00004 1953 2066 len=111
115 GTGCGCGAGAAAAAACTACGCGTTAACCGCCAATTTTCACTTCCCCACAGATCTGTCTCG
116 AGATTCTCGAGTCATTTTTCAAGTTTATTTGTTTGTCAGCGGTTGTTTTAT
117 .....
118 ]]></help>
119 <expand macro="citation" />
120 </tool>