Mercurial > repos > yhoogstrate > segmentation_fold

annotate utils_estimate-energy.xml @ 26:660c25c66c8a draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/segmentation_fold commit 3a3c1d069e0a079d8ea7c0b4ac856ef24141b1aa
author erasmus-medical-center
date Fri, 24 Feb 2017 04:18:08 -0500
parents 44330a54b8eb
children
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1 <tool id="smf_utils_estimate-energy" name="estimate-energy" version="@VERSION@-2">
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2 <description>Estimates whether a certain Segment(Loop) is present and for which delta-G this transistion takes place</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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11 <command detect_errors="aggressive"><![CDATA[
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12 segmentation-fold-utils
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13 estimate-energy
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14 -T \${GALAXY_SLOTS:-2}
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15 -x
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16 #if str($parameters.use_custom_xml) == "true"
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17 "${parameters.input_xml}"
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18 #else
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19 "\$(segmentation-fold -X)"
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20 #end if
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22 -p $precision
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23 -r $randomize
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25 #if $sequences_from_fasta_file:
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26 --sequences-from-fasta-file "${sequences_from_fasta_file}"
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27 #end if
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29 $output_list
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30 ]]></command>
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32 <inputs>
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33 <conditional name="parameters">
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34 <param name="use_custom_xml"
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35 type="boolean"
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36 truevalue="true"
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37 falsevalue="false"
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38 checked="false"
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39 label="Use segment definition from history" />
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41 <when value="false" />
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42 <when value="true">
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43 <param name="input_xml"
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44 type="data"
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45 format="xml"
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46 multiple="false"
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47 argument="-x"
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48 label="Custom 'segments.xml'-syntaxed file" />
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49 </when>
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50 </conditional>
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51
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52 <param name="precision"
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53 type="float"
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54 value="0.05"
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55 min="0"
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56 argument="--precision"
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57 label="Precision"
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58 help="Minimal difference for binary split - the smaller this value the slower. if this value equals 0, the difference is set to infinity (default: 0.05)" />
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59
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60 <param name="randomize"
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61 type="integer"
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62 value="0"
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63 min="0"
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64 argument="--randomize"
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65 label="Shuffle each sequence this many times and predict energy of shuffled sequence(s) (default: 0, 0 means disabled)" />
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66
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67 <param name="sequences_from_fasta_file"
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68 type="data"
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69 format="fasta"
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70 multiple="false"
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71 optional="true"
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72 argument="--sequences-from-fasta-file"
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73 label="Optional sequences to scan for Segment(Loop)s (FASTA)"
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74 help="Use sequences from a FASTA file instead of the XML file that contains the segments. In XML files you can explicitly link one Segment(Loop) to one particular sequence instead of doing n*n comparisons (default: None)" />
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75 </inputs>
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76
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77 <outputs>
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78 <data format="dbn" name="output_list" label="${tool.name}" />
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79 </outputs>
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81 <tests>
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82 <!-- xml * fasta mode -->
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83 <test>
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84 <param name="use_custom_xml" value="false" ftype="fasta" />
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85 <param name="sequences_from_fasta_file" value="SNORD13-revised.fa" ftype="fasta" />
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86
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87 <output name="output_list" file="SNORD13-revised.scan-for-segments.txt" />
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88 </test>
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89 <test>
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90 <param name="use_custom_xml" value="false" ftype="fasta" />
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91 <param name="sequences_from_fasta_file" value="SNORD48-revised.fa" ftype="fasta" />
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92
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93 <output name="output_list" file="SNORD48-revised.scan-for-segments.txt" />
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94 </test>
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95 <test>
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96 <param name="use_custom_xml" value="false" ftype="fasta" />
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97 <param name="sequences_from_fasta_file" value="SNORD114-4-revised.fa" ftype="fasta" />
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98
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99 <output name="output_list" file="SNORD114-4-revised.scan-for-segments.txt" />
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100 </test>
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101 <test>
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102 <param name="use_custom_xml" value="false" ftype="fasta" />
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103 <param name="sequences_from_fasta_file" value="SNORD118-revised.fa" ftype="fasta" />
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104
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105 <output name="output_list" file="SNORD118-revised.scan-for-segments.txt" />
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106 </test>
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107
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108
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109 <!-- xml * xml mode -->
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110 <test>
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111 <param name="use_custom_xml" value="true" />
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112 <param name="input_xml" value="segments_truncated.xml" ftype="xml" />
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113 <param name="do_randomization" value="false" />
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114 <param name="shuffle_n_times" value="0" />
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115
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116 <output name="output_list" file="segments_truncated.out.txt" lines_diff="2" />
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117 </test>
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118 <test>
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119 <param name="use_custom_xml" value="true" />
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120 <param name="input_xml" value="segments_truncated.xml" ftype="xml" />
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121 <param name="do_randomization" value="false" />
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122 <param name="shuffle_n_times" value="1" />
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123
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124 <output name="output_list" file="segments_truncated.2.out.txt" lines_diff="10" />
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125 </test>
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126 </tests>
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127
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128 <help><![CDATA[
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129 This is an utility of the segmentation-fold package that allows to scan for the presence of certain segments.
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130 If present, it will also scan for the Gibbs free energy necessairy the segment has to provide to contribute to the optimal structure.
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131 ]]></help>
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132
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133 <expand macro="citations" />
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134 </tool>