Mercurial > repos > yhoogstrate > segmentation_fold

annotate utils_estimate-energy.xml @ 12:c690aa928d3d draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
author yhoogstrate
date Fri, 06 May 2016 06:08:36 -0400
parents 487f438da099
children 7e5b96d45f8d
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12
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1 <tool id="smf_utils_estimate-energy" name="estimate-energy" version="@VERSION@-1">
11
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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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3
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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 <requirements>
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9 @REQUIREMENTS_SMF@
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10 @REQUIREMENTS_UTILS@
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11 </requirements>
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12 <expand macro="stdio" />
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14 <version_command>echo $(@VERSION_COMMAND_SMF@)", "$(@VERSION_COMMAND_UTILS@)</version_command>
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16 <command><![CDATA[
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17 segmentation-fold-utils
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18 estimate-energy
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19 -T \${GALAXY_SLOTS:-2}
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20 -x
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21 #if str($parameters.use_custom_xml) == "true"
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22 "${parameters.input_xml}"
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23 #else
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24 "\$SEGMENTATION_FOLD_DEFAULT_XML"
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25 #end if
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26
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27 -p $precision
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28 -r $randomize
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29
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30 #if $sequences_from_fasta_file:
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31 --sequences-from-fasta-file "${sequences_from_fasta_file}"
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32 #end if
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33
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34 $output_list
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35 ]]></command>
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36
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37 <inputs>
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38 <conditional name="parameters">
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39 <param name="use_custom_xml"
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40 type="boolean"
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41 truevalue="true"
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42 falsevalue="false"
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43 selected="false"
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44 label="Use segment definition from history" />
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45
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46 <when value="false" />
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47 <when value="true">
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48 <param name="input_xml"
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49 type="data"
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50 format="xml"
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51 multiple="false"
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52 argument="-x"
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53 label="Custom 'segments.xml'-syntaxed file" />
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54 </when>
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55 </conditional>
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56
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57 <param name="precision"
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58 type="float"
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59 value="0.05"
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60 min="0"
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61 argument="--precision"
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62 label="Precision"
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63 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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64
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65 <param name="randomize"
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66 type="integer"
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67 value="0"
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68 min="0"
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69 argument="--randomize"
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70 label="Shuffle each sequence this many times and predict energy of shuffled sequence(s)·(default:·0,·0·means·disabled)" />
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71
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72 <param name="sequences_from_fasta_file"
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73 type="data"
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74 format="fasta"
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75 multiple="false"
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76 optional="true"
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77 argument="--sequences-from-fasta-file"
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78 label="Optional sequences to scan for Segment(Loop)s (FASTA)"
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79 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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80 </inputs>
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81
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82 <outputs>
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83 <data format="dbn" name="output_list" label="${tool.name}" />
11
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84 </outputs>
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85
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86 <tests>
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87 <!-- xml * fasta mode -->
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88 <test>
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89 <param name="use_custom_xml" value="false" ftype="fasta" />
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90 <param name="sequences_from_fasta_file" value="SNORD13-revised.fa" ftype="fasta" />
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91
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92 <output name="output_list" file="SNORD13-revised.scan-for-segments.txt" />
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93 </test>
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94 <test>
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95 <param name="use_custom_xml" value="false" ftype="fasta" />
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96 <param name="sequences_from_fasta_file" value="SNORD48-revised.fa" ftype="fasta" />
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97
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98 <output name="output_list" file="SNORD48-revised.scan-for-segments.txt" />
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99 </test>
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100 <test>
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101 <param name="use_custom_xml" value="false" ftype="fasta" />
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102 <param name="sequences_from_fasta_file" value="SNORD114-4-revised.fa" ftype="fasta" />
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103
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104 <output name="output_list" file="SNORD114-4-revised.scan-for-segments.txt" />
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105 </test>
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106 <test>
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107 <param name="use_custom_xml" value="false" ftype="fasta" />
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108 <param name="sequences_from_fasta_file" value="SNORD118-revised.fa" ftype="fasta" />
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109
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110 <output name="output_list" file="SNORD118-revised.scan-for-segments.txt" />
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111 </test>
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112
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113
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114 <!-- xml * xml mode -->
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115 <test>
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116 <param name="use_custom_xml" value="true" />
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117 <param name="input_xml" value="segments_truncated.xml" ftype="xml" />
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118 <param name="do_randomization" value="false" />
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119 <param name="shuffle_n_times" value="0" />
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120
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121 <output name="output_list" file="segments_truncated.out.txt" lines_diff="2" />
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122 </test>
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123 <test>
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124 <param name="use_custom_xml" value="true" />
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125 <param name="input_xml" value="segments_truncated.xml" ftype="xml" />
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126 <param name="do_randomization" value="false" />
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127 <param name="shuffle_n_times" value="1" />
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128
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129 <output name="output_list" file="segments_truncated.2.out.txt" lines_diff="10" />
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130 </test>
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131 </tests>
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132
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133 <help><![CDATA[
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134 This is an utility of the segmentation-fold package that allows to scan for the presence of certain segments.
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135 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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136 ]]></help>
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137
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138 <expand macro="citations" />
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139 </tool>