annotate macros.xml @ 0:b4310d79bbfb draft default tip

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