annotate rnalfold.xml @ 3:04c56f5b0907 draft default tip

Uploaded
author rnateam
date Fri, 13 Feb 2015 04:08:49 -0500
parents 5e58cbf27a05
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
1 <tool id="rnalfold" name="RNALfold" version="2.1.6.0">
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
2 <description>calculates locally stable secondary structures of RNA</description>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
3 <expand macro="requirements" />
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
4 <expand macro="version_command" />
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
5 <expand macro="stdio" />
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
6 <macros>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
7 <token name="@EXECUTABLE@">RNALfold</token>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
8 <import>macros.xml</import>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
9 </macros>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
10 <command>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
11 <![CDATA[
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
12 RNALfold -L $span -T $temperature -d$dangling < $fasta_input | sed -r 's/(^[.()]*) +(\(.*\)) +(.*)/\1\t\2\t\3/' > $out_file
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
13 #if $varExists('$advancedOptions.noconversion')
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
14 #if $advancedOptions.noconversion
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
15 --noconv
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
16 #end if
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
17 #if $advancedOptions.gquad
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
18 --gquad
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
19 #end if
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
20 #if $advancedOptions.nolp
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
21 --noLP
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
22 #end if
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
23 #if $advancedOptions.nogu
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
24 --noGU
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
25 #end if
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
26 #if $advancedOptions.noclosinggu
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
27 --noClosingGU
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
28 #end if
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
29 #if $advancedOptions.notetra
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
30 --noTetra
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
31 #end if
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
32 #end if
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
33 ]]>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
34 </command>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
35 <inputs>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
36 <param format="fasta" name="fasta_input" type="data" label="FASTA file"/>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
37 <param name="span" type="integer" min="0" max="5000" value="150" label="base pair span" help="Maximal distance between two paired bases. (-L)"/>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
38 <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
39 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
40 <option value="2" selected="true">unpaired bases participate in all dangling ends (2)</option>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
41 <option value="0">ignore dangling ends (0)</option>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
42 <option value="1">unpaired bases participate in one dangling end only (1)</option>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
43 <option value="3">allow coaxial stacking (3)</option>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
44 </param>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
45 <conditional name="advancedOptions">
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
46 <param name="advancedSelector" type="select" label="advanced options">
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
47 <option value="basic">basic Options</option>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
48 <option value="advanced">advanced Options</option>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
49 </param>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
50 <when value="advanced">
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
51 <param name="noconversion" type="boolean" checked="false" label="no conversion" help="--noconv do not convert thymine to uracile (T -> U)."/>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
52 <param name="gquad" type="boolean" checked="false" label="G Quadruplex formation" help="-g take into account G Quadruplex formation"/>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
53 <param name="nolp" type="boolean" checked="false" label="No lonely pairs" help="--noLP don't allow lonely pairs."/>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
54 <param name="nogu" type="boolean" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
55 <param name="noclosinggu" type="boolean" checked="false" label="No GU pairing at the ends" help="--noClosingGU don't allow pairing of G and U at the ends of helices."/>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
56 <param name="notetra" type="boolean" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
57 </when>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
58 </conditional>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
59 </inputs>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
60 <outputs>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
61 <data format="txt" name="out_file"/>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
62 </outputs>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
63 <tests>
2
5e58cbf27a05 Uploaded
rnateam
parents: 0
diff changeset
64 <test>
5e58cbf27a05 Uploaded
rnateam
parents: 0
diff changeset
65 <param name="fasta_input" value="rnalfold_input1.fa"/>
5e58cbf27a05 Uploaded
rnateam
parents: 0
diff changeset
66 <output name="out_file" file="rnalfold_result1.txt"/>
5e58cbf27a05 Uploaded
rnateam
parents: 0
diff changeset
67 </test>
0
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
68 </tests>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
69 <help>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
70 <![CDATA[
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
71 **RNALfold**
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
72
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
73 Compute locally stable RNA secondary structure with a maximal base pair span.
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
74 For a sequence of length n and a base pair span of L the algorithm uses only
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
75 O(n+L*L) memory and O(n*L*L) CPU time. *Thus it is practical to "scan" very
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
76 large genomes for short RNA structures*.
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
77 Output consists of a list of secondary structure components of size <= L, one
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
78 entry per line. Each output line contains the predicted local structure its
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
79 energy in kcal/mol and the starting position of the local structure.
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
80
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
81 -----
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
82
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
83 **Input format**
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
84
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
85 - RNALfold requires one input file in FASTA format
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
86
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
87 ------
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
88
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
89 **Outputs**
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
90
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
91 - text output with dot-bracket notation and free energies of the secondary structures
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
92
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
93 ]]>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
94 </help>
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
95 <expand macro="requirements" />
78d673470d45 Imported from capsule None
rnateam
parents:
diff changeset
96 </tool>