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annotate macros.xml @ 0:74fa55f35f0d 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 bgruening
date Tue, 06 Dec 2016 11:38:49 -0500
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74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
bgruening
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1 <macros>
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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2 <token name="@VERSION@">1.8.12</token>
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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3
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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4 <xml name="requirements">
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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5 <requirements>
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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6 <requirement type="package" version="@VERSION@">locarna</requirement>
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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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:" />
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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13 </stdio>
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14 </xml>
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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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[
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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19 mlocarna --version
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20 ]]>
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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21 </version_command>
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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22 </xml>
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23
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24 <xml name="common_scoring_parameters">
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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25 <param name="struct_weight" argument="struct-weight"
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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26 label="Structure weight" type="integer"
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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27 value="200" min="0" max="800" />
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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28 <param name="indel_opening" argument="indel-opening"
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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29 label="Indel opening score" type="integer"
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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30 value="-500" max="0" min="-1500" />
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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31 <param argument="indel" label="Indel score" type="integer"
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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32 value="-350" min="-1000" max="0" />
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33 <param argument="tau" type="integer" value="50"
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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34 min="0" max="200"
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35 label="Sequence contribution at structure match in percent"/>
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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36
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37 <conditional name="sequence_score">
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38 <param name="sequence_score_selector" type="select" label="Type of sequence score contribution">
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39 <option value="ribofit">Use ribofit</option>
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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40 <option value="ribosum">Use RIBOSUM85_60</option>
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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41 <option value="match">Simple match/mismatch costs</option>
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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42 </param>
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43 <when value="ribofit" />
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44 <when value="ribosum" />
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45 <when value="match">
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46 <param name="match" type="integer" value="50"
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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47 min="0" max="400"
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48 label="Match score" />
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49 <param name="mismatch" type="integer" value="0"
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50 min="-400" max="0"
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51 label="Mismatch score" />
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52 </when>
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53 </conditional>
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54 </xml>
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55
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56 <xml name="common_folding_parameters">
74fa55f35f0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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57 <param name="plfold_span" argument="--plfold-span"
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58 type="integer" value="150" min="-1" max="400"
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59 label="Maximum basepair span (local folding); -1 for global folding" />
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60
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61 <param name="plfold_winsize" argument="--plfold-winsize"
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62 type="integer" value="300" min="-1" max="800"
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63 label="Window size for local folding" />
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64
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65 <param name="rnafold_temperature" argument="rnafold-temperature"
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66 type="float" value="37.0" min="10" max="50"
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67 label="Temperature for RNAfold (RNAfold's -T option)" />
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68 </xml>
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69
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70 <xml name="common_heuristic_parameters">
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71 <param name="min_prob" argument="min-prob" type="float" value="0.0005"
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72 min="0.0" max="0.2"
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73 label="Minimal / cutoff probability" />
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74
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75 <param name="max_diff_am" argument="max-diff-am"
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76 type="integer" value="30"
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77 min="-1" max="300"
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78 label="Maximal difference for sizes of matched arcs (-1=off)" />
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79 <param name="max_diff" argument="max-diff" type="integer"
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80 value="60" min="-1" max="300"
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81 label="Maximal difference for alignment traces (-1=off)" />
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82
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83 <param name="max_diff_at_am" argument="max-diff-am" type="integer"
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84 value="-1" min="-1" max="300"
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85 label="Maximal difference for alignment traces, only at arc match positions" />
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86
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87 <param name="max_bps_length_ratio" argument="max-bps-length-ratio"
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88 type="float" value="0.0" min="0.0" max="1.0"
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89 label="Maximal ratio of #base pairs divided by sequence length (default: no effect)" />
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90
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91 <param name="alifold_consensus_dp" argument="alifold-consensus-dp"
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92 type="boolean" checked="false"
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93 truevalue="--alifold-consensus-dp" falsevalue=""
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94 label="Compute consensus dot plot by alifold" />
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95 </xml>
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96
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97 <xml name="common_other_parameters">
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98 </xml>
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99
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100 <xml name="common_outputs">
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101 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
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102 <filter>stdout_verbosity != '--quiet'</filter>
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103 </data>
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104 <data format="clustal" name="clustal" from_work_dir="outdir/results/result.aln"
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105 label="${tool.name} alignment (clustal) on ${on_string}">
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106 <filter>'clustal' in outputs</filter>
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107 </data>
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108 <data format="stockholm" name="stockholm" from_work_dir="outdir/results/result.stk"
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109 label="${tool.name} alignment (stockholm) on ${on_string}">
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110 <filter>'stockholm' in outputs</filter>
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111 </data>
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112 </xml>
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113
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114 <xml name="citations">
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115 <citations>
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116 <citation
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117 type="doi">10.1371/journal.pcbi.0030065</citation>
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118 <citation type="doi">10.1261/rna.029041.111</citation>
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119 </citations>
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120 </xml>
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121
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122
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123
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124 </macros>
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125