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comparison macros.xml @ 0:59055c49a112 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
author rnateam
date Tue, 06 Dec 2016 11:39:14 -0500
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-1:000000000000 0:59055c49a112
1 <macros>
2 <token name="@VERSION@">1.8.12</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="common_scoring_parameters">
25 <param name="struct_weight" argument="struct-weight"
26 label="Structure weight" type="integer"
27 value="200" min="0" max="800" />
28 <param name="indel_opening" argument="indel-opening"
29 label="Indel opening score" type="integer"
30 value="-500" max="0" min="-1500" />
31 <param argument="indel" label="Indel score" type="integer"
32 value="-350" min="-1000" max="0" />
33 <param argument="tau" type="integer" value="50"
34 min="0" max="200"
35 label="Sequence contribution at structure match in percent"/>
36
37 <conditional name="sequence_score">
38 <param name="sequence_score_selector" type="select" label="Type of sequence score contribution">
39 <option value="ribofit">Use ribofit</option>
40 <option value="ribosum">Use RIBOSUM85_60</option>
41 <option value="match">Simple match/mismatch costs</option>
42 </param>
43 <when value="ribofit" />
44 <when value="ribosum" />
45 <when value="match">
46 <param name="match" type="integer" value="50"
47 min="0" max="400"
48 label="Match score" />
49 <param name="mismatch" type="integer" value="0"
50 min="-400" max="0"
51 label="Mismatch score" />
52 </when>
53 </conditional>
54 </xml>
55
56 <xml name="common_folding_parameters">
57 <param name="plfold_span" argument="--plfold-span"
58 type="integer" value="150" min="-1" max="400"
59 label="Maximum basepair span (local folding); -1 for global folding" />
60
61 <param name="plfold_winsize" argument="--plfold-winsize"
62 type="integer" value="300" min="-1" max="800"
63 label="Window size for local folding" />
64
65 <param name="rnafold_temperature" argument="rnafold-temperature"
66 type="float" value="37.0" min="10" max="50"
67 label="Temperature for RNAfold (RNAfold's -T option)" />
68 </xml>
69
70 <xml name="common_heuristic_parameters">
71 <param name="min_prob" argument="min-prob" type="float" value="0.0005"
72 min="0.0" max="0.2"
73 label="Minimal / cutoff probability" />
74
75 <param name="max_diff_am" argument="max-diff-am"
76 type="integer" value="30"
77 min="-1" max="300"
78 label="Maximal difference for sizes of matched arcs (-1=off)" />
79 <param name="max_diff" argument="max-diff" type="integer"
80 value="60" min="-1" max="300"
81 label="Maximal difference for alignment traces (-1=off)" />
82
83 <param name="max_diff_at_am" argument="max-diff-am" type="integer"
84 value="-1" min="-1" max="300"
85 label="Maximal difference for alignment traces, only at arc match positions" />
86
87 <param name="max_bps_length_ratio" argument="max-bps-length-ratio"
88 type="float" value="0.0" min="0.0" max="1.0"
89 label="Maximal ratio of #base pairs divided by sequence length (default: no effect)" />
90
91 <param name="alifold_consensus_dp" argument="alifold-consensus-dp"
92 type="boolean" checked="false"
93 truevalue="--alifold-consensus-dp" falsevalue=""
94 label="Compute consensus dot plot by alifold" />
95 </xml>
96
97 <xml name="common_other_parameters">
98 </xml>
99
100 <xml name="common_outputs">
101 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
102 <filter>stdout_verbosity != '--quiet'</filter>
103 </data>
104 <data format="clustal" name="clustal" from_work_dir="outdir/results/result.aln"
105 label="${tool.name} alignment (clustal) on ${on_string}">
106 <filter>'clustal' in outputs</filter>
107 </data>
108 <data format="stockholm" name="stockholm" from_work_dir="outdir/results/result.stk"
109 label="${tool.name} alignment (stockholm) on ${on_string}">
110 <filter>'stockholm' in outputs</filter>
111 </data>
112 </xml>
113
114 <xml name="citations">
115 <citations>
116 <citation
117 type="doi">10.1371/journal.pcbi.0030065</citation>
118 <citation type="doi">10.1261/rna.029041.111</citation>
119 </citations>
120 </xml>
121
122
123
124 </macros>
125