Mercurial > repos > bgruening > locarna_pairwise

comparison macros.xml @ 0:b4310d79bbfb draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
author bgruening
date Wed, 28 Dec 2016 18:48:14 -0500
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-1:000000000000 0:b4310d79bbfb
1 <macros>
2 <token name="@VERSION@">1.9.0</token>
3
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@VERSION@">locarna</requirement>
7 </requirements>
8 </xml>
9
10 <xml name="stdio">
11 <stdio>
12 <exit_code range="1:" />
13 </stdio>
14 </xml>
15
16 <xml name="version">
17 <version_command>
18 <![CDATA[
19 mlocarna --version
20 ]]>
21 </version_command>
22 </xml>
23
24 <xml name="bed_anchors">
25 <conditional name="bed_anchors">
26 <param name="bed_anchors_selector" type="select" label="Anchor constraints"
27 help="Anchor constraints in bed format specify positions of
28 named anchor regions per sequence. The sequence names
29 ('contig' names have to correspond to the fasta input
30 sequence names. Anchor names must be unique per sequence
31 and regions of the same name for different sequences
32 must have the same length. This constrains the alignment
33 to align all regions of the same name.">
34 <option value="no">Don't load anchor constraints from bed file</option>
35 <option value="yes">Load anchor constraints from bed file</option>
36 </param>
37 <when value="no" />
38 <when value="yes">
39 <param name="bed_anchors_file" type="data" format="tabular"
40 label="Anchor constraint specification in bed format"
41 />
42 </when>
43 </conditional>
44 </xml>
45
46 <xml name="common_scoring_parameters">
47 <param name="struct_weight" argument="struct-weight"
48 label="Structure weight" type="integer"
49 value="200" min="0" max="800" />
50 <param name="indel_opening" argument="indel-opening"
51 label="Indel opening score" type="integer"
52 value="-500" max="0" min="-1500" />
53 <param argument="indel" label="Indel score" type="integer"
54 value="-350" min="-1000" max="0" />
55 <param argument="tau" type="integer" value="50"
56 min="0" max="200"
57 label="Sequence contribution at structure match in percent"/>
58
59 <conditional name="sequence_score">
60 <param name="sequence_score_selector" type="select" label="Type of sequence score contribution">
61 <option value="ribofit">Use ribofit</option>
62 <option value="ribosum">Use RIBOSUM85_60</option>
63 <option value="match">Simple match/mismatch costs</option>
64 </param>
65 <when value="ribofit" />
66 <when value="ribosum" />
67 <when value="match">
68 <param name="match" type="integer" value="50"
69 min="0" max="400"
70 label="Match score" />
71 <param name="mismatch" type="integer" value="0"
72 min="-400" max="0"
73 label="Mismatch score" />
74 </when>
75 </conditional>
76 </xml>
77
78 <xml name="plfolding_parameters">
79 <param name="plfold_span" argument="--plfold-span"
80 type="integer" value="150" min="-1" max="400"
81 label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />
82
83 <param name="plfold_winsize" argument="--plfold-winsize"
84 type="integer" value="300" min="-1" max="800"
85 label="Window size for local folding" />
86 </xml>
87
88 <xml name="common_folding_parameters">
89 <param name="rnafold_temperature" argument="rnafold-temperature"
90 type="float" value="37.0" min="10" max="50"
91 label="Temperature for RNAfold (RNAfold's -T option)" />
92 </xml>
93
94 <xml name="common_heuristic_parameters">
95 <param name="min_prob" argument="min-prob" type="float" value="0.0005"
96 min="0.0" max="0.2"
97 label="Minimal / cutoff probability" />
98
99 <param name="max_diff_am" argument="max-diff-am"
100 type="integer" value="30"
101 min="-1" max="300"
102 label="Maximal difference for sizes of matched arcs (-1=off)" />
103
104 <param name="max_diff" argument="max-diff" type="integer"
105 value="60" min="-1" max="300"
106 label="Maximal difference for alignment traces (-1=off)" />
107
108 <param name="max_diff_at_am" argument="max-diff-am" type="integer"
109 value="-1" min="-1" max="300"
110 label="Maximal difference for alignment traces, only at arc match positions" />
111
112 <param name="max_bps_length_ratio" argument="max-bps-length-ratio"
113 type="float" value="0.0" min="0.0" max="1.0"
114 label="Maximal ratio of #base pairs divided by sequence length (default: no effect)" />
115 </xml>
116
117 <xml name="alifold_consensus_parameter">
118 <param name="alifold_consensus_dp" argument="alifold-consensus-dp"
119 type="boolean" checked="false"
120 truevalue="--alifold-consensus-dp" falsevalue=""
121 label="Compute consensus dot plot by alifold" />
122 </xml>
123
124 <xml name="constraints">
125 <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP"
126 checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" />
127 <param name="maxBPspan" argument="--maxBPspan"
128 type="integer" value="-1" min="-1" max="400"
129 label="Maximum basepair span by RNAfold; -1 for arbitrary span" />
130 <param name="ignore_constraints" argument="ignore-constraints"
131 type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue=""
132 help="Ignore all anchor and structure constraints given
133 in the fasta(-ish) input." />
134 </xml>
135
136 <xml name="common_other_parameters">
137 </xml>
138
139 <xml name="common_outputs">
140 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
141 <filter>stdout_verbosity != '--quiet'</filter>
142 </data>
143 <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"
144 label="${tool.name} alignment (annotated clustal) on ${on_string}">
145 <filter>'clustal' in outputs</filter>
146 </data>
147 <data format="clustal" name="clustal_strict"
148 from_work_dir="mlocarna_results/results/result.strict-aln"
149 label="${tool.name} alignment (clustal) on ${on_string}">
150 <filter>'clustal_strict' in outputs</filter>
151 </data>
152 <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk"
153 label="${tool.name} alignment (stockholm) on ${on_string}">
154 <filter>'stockholm' in outputs</filter>
155 </data>
156 <data format="txt" name="pp"
157 from_work_dir="mlocarna_results/results/result.pp"
158 label="${tool.name} alignment (PP 2.0) on ${on_string}">
159 <filter>'pp' in outputs</filter>
160 </data>
161 <data format="tar.gz" name="mlocarna_results_tgz"
162 label="${tool.name} results archive on ${on_string}">
163 <filter>'mlocarna_results' in outputs</filter>
164 </data>
165 </xml>
166
167 <xml name="citations">
168 <citations>
169 <citation
170 type="doi">10.1371/journal.pcbi.0030065</citation>
171 <citation type="doi">10.1261/rna.029041.111</citation>
172 </citations>
173 </xml>
174
175
176
177 </macros>
178