Mercurial > repos > yhoogstrate > segmentation_fold

annotate utils_estimate-energy.xml @ 21:04ca0b1c5c91 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 3814f709ce964e99fe3cf2f979c11f8f3b87bce3-dirty
author yhoogstrate
date Tue, 24 May 2016 07:42:09 -0400
parents 3fbde4864e00
children 23cad8b78b74
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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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8 <requirements>
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9 <requirement type="package" version="2.7.10">python</requirement>
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10 <requirement type="package" version="1.9">numpy</requirement>
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11 <requirement type="package" version="0.8.2.1">pysam</requirement>
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12 <requirement type="package" version="0.6.1">htseq</requirement>
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13 <requirement type="package" version="2.0.0">segmentation-fold-utils</requirement>
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15 <requirement type="package" version="1.6.5">segmentation-fold</requirement>
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16 </requirements>
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17 <expand macro="stdio" />
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19 <version_command>echo $(@VERSION_COMMAND_SMF@)", "$(@VERSION_COMMAND_UTILS@)</version_command>
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21 <command><![CDATA[
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22 segmentation-fold-utils
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23 estimate-energy
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24 -T \${GALAXY_SLOTS:-2}
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25 -x
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26 #if str($parameters.use_custom_xml) == "true"
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27 "${parameters.input_xml}"
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28 #else
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29 "\$SEGMENTATION_FOLD_DEFAULT_XML"
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30 #end if
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31
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32 -p $precision
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33 -r $randomize
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34
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35 #if $sequences_from_fasta_file:
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36 --sequences-from-fasta-file "${sequences_from_fasta_file}"
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37 #end if
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38
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39 $output_list
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40 ]]></command>
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41
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42 <inputs>
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43 <conditional name="parameters">
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44 <param name="use_custom_xml"
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45 type="boolean"
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46 truevalue="true"
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47 falsevalue="false"
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48 selected="false"
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49 label="Use segment definition from history" />
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50
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51 <when value="false" />
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52 <when value="true">
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53 <param name="input_xml"
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54 type="data"
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55 format="xml"
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56 multiple="false"
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57 argument="-x"
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58 label="Custom 'segments.xml'-syntaxed file" />
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59 </when>
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60 </conditional>
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61
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62 <param name="precision"
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63 type="float"
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64 value="0.05"
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65 min="0"
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66 argument="--precision"
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67 label="Precision"
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68 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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69
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70 <param name="randomize"
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71 type="integer"
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72 value="0"
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73 min="0"
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74 argument="--randomize"
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75 label="Shuffle each sequence this many times and predict energy of shuffled sequence(s)·(default:·0,·0·means·disabled)" />
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76
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77 <param name="sequences_from_fasta_file"
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78 type="data"
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79 format="fasta"
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80 multiple="false"
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81 optional="true"
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82 argument="--sequences-from-fasta-file"
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83 label="Optional sequences to scan for Segment(Loop)s (FASTA)"
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84 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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85 </inputs>
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86
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87 <outputs>
12
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88 <data format="dbn" name="output_list" label="${tool.name}" />
11
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89 </outputs>
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90
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91 <tests>
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92 <!-- xml * fasta mode -->
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93 <test>
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94 <param name="use_custom_xml" value="false" ftype="fasta" />
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95 <param name="sequences_from_fasta_file" value="SNORD13-revised.fa" ftype="fasta" />
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96
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97 <output name="output_list" file="SNORD13-revised.scan-for-segments.txt" />
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98 </test>
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99 <test>
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100 <param name="use_custom_xml" value="false" ftype="fasta" />
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101 <param name="sequences_from_fasta_file" value="SNORD48-revised.fa" ftype="fasta" />
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102
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103 <output name="output_list" file="SNORD48-revised.scan-for-segments.txt" />
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104 </test>
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105 <test>
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106 <param name="use_custom_xml" value="false" ftype="fasta" />
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107 <param name="sequences_from_fasta_file" value="SNORD114-4-revised.fa" ftype="fasta" />
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108
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109 <output name="output_list" file="SNORD114-4-revised.scan-for-segments.txt" />
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110 </test>
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111 <test>
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112 <param name="use_custom_xml" value="false" ftype="fasta" />
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113 <param name="sequences_from_fasta_file" value="SNORD118-revised.fa" ftype="fasta" />
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114
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115 <output name="output_list" file="SNORD118-revised.scan-for-segments.txt" />
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116 </test>
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117
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118
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119 <!-- xml * xml mode -->
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120 <test>
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121 <param name="use_custom_xml" value="true" />
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122 <param name="input_xml" value="segments_truncated.xml" ftype="xml" />
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123 <param name="do_randomization" value="false" />
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124 <param name="shuffle_n_times" value="0" />
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125
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126 <output name="output_list" file="segments_truncated.out.txt" lines_diff="2" />
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127 </test>
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128 <test>
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129 <param name="use_custom_xml" value="true" />
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130 <param name="input_xml" value="segments_truncated.xml" ftype="xml" />
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131 <param name="do_randomization" value="false" />
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132 <param name="shuffle_n_times" value="1" />
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133
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134 <output name="output_list" file="segments_truncated.2.out.txt" lines_diff="10" />
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135 </test>
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136 </tests>
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137
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138 <help><![CDATA[
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139 This is an utility of the segmentation-fold package that allows to scan for the presence of certain segments.
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140 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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141 ]]></help>
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142
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143 <expand macro="citations" />
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144 </tool>