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annotate fasttree.xml @ 0:614a12d56e58 draft default tip

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planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc/tree/master/tools/fasttree commit 4db125fcd73327813d7bd511852bbe9ffc68a25c
author sanbi-uwc
date Mon, 09 Jan 2017 08:07:45 -0500
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614a12d56e58 planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc/tree/master/tools/fasttree commit 4db125fcd73327813d7bd511852bbe9ffc68a25c
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1 <tool id="fasttree" name="FastTree" version="0.1">
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2 <description>infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.</description>
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3
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4 <requirements>
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5 <requirement type="package" version="2.1.9">fasttree</requirement>
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6 </requirements>
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7
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8 <command detect_errors="aggressive">
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9 <![CDATA[
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10 OMP_NUM_THREADS=\${GALAXY_SLOTS:-1} &&
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11 export OMP_NUM_THREADS &&
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12 FastTreeMP
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13 #if ( ( str( $advanced_options.advanced_options_selector ) == 'false'
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14 and str( $advanced_options.alignment_type1 ) == 'nucl' ) or
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15 ( str( $advanced_options.advanced_options_selector ) == 'true'
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16 and str( $advanced_options.alignment_type_selection.alignment_type2 ) == 'nucl' ) ):
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17 -nt
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18 #end if
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19 #if str( $advanced_options.advanced_options_selector ) == 'true':
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20 $advanced_options.fastest
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21 $advanced_options.gamma
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22 $advanced_options.noml
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23 $advanced_options.nosupport
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24 $advanced_options.log
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25 #if str( $advanced_options.alignment_type_selection.alignment_type2 ) == 'nucl':
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26 $advanced_options.alignment_type_selection.nucl_alignment_model
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27 #else
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28 $advanced_options.alignment_type_selection.prot_alignment_model
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29 #end if
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30 #end if
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31 '${input_alignment}' > '${output_tree}'
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32 ]]>
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33 </command>
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34
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35 <inputs>
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36 <param name="input_alignment" type="data" format="fasta,phylip"
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37 label="Multiple sequence alignment"/>
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38 <conditional name="advanced_options">
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39 <param name="advanced_options_selector" type="select" label="Advanced options">
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40 <option value="true">Yes</option>
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41 <option value="false" selected="True">No</option>
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42 </param>
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43 <when value="true">
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44 <param argument="-fastest" type="boolean" truevalue="-fastest" falsevalue=""
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45 label="Fastest mode (recommended for > 50,000 sequences)"/>
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46 <param argument="-gamma" type="boolean" truevalue="-gamma" falsevalue=""
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47 label="Rescale likelihoods using Gamma20 model" />
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48 <param argument="-noml" type="boolean" truevalue="-noml" falsevalue=""
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49 label="Disable Maximum-Likelihood topology refinement step" />
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50 <param argument="-nosupport" type="boolean" truevalue="-nosupport" falsevalue=""
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51 label="Disable computation of support values for tree splits" />
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52 <param argument="-log" type="boolean" truevalue="-log output_log.txt" falsevalue=""
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53 label="Save log file" />
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54 <conditional name="alignment_type_selection">
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55 <param name="alignment_type2" type="select" label="Alignment type">
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56 <option value="nucl">Nucleotide</option>
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57 <option value="prot" selected="True">Protein</option>
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58 </param>
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59 <when value="nucl">
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60 <param name="nucl_alignment_model" label="Alignment model" type="select">
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61 <option value="" selected="True">Jukes-Cantor+CAT</option>
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62 <option value="-gtr">GTR+CAT</option>
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63 </param>
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64 </when>
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65 <when value="prot">
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66 <param name="prot_alignment_model" label="Alignment model" type="select">
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67 <option value="">JTT+CAT</option>
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68 <option value="-wag">WAG+CAT</option>
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69 <option value="-lg">LG+CAT</option>
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70 </param>
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71 </when>
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72 </conditional>
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73 </when>
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74 <when value="false">
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75 <param name="alignment_type1" type="select" label="Alignment type">
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76 <option value="nucl">Nucleotide</option>
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77 <option value="prot" selected="True">Protein</option>
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78 </param>
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79 </when>
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80 </conditional>
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81
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82 </inputs>
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83
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84 <outputs>
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85 <data name="output_tree" format="nhx" />
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86 <data name="output_log" format="txt" label="Log from ${tool.name} on ${on_string}" from_work_dir="output_log.txt">
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87 <filter>advanced_options['advanced_options_selector'] == 'true' and advanced_options['log'] is True</filter>
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88 </data>
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89 </outputs>
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90
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91 <tests>
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92 <test>
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93 <param name="input_alignment" value="sample_aln1.fasta" ftype="fasta" />
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94 <param name="advanced_options_selector" value="false" />
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95 <param name="alignment_type1" value="nucl" />
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96 <output name="output_tree">
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97 <assert_contents>
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98 <has_text_matching expression="^^\(\(\(471528:[^,]+,\(\(484305:[^,]+,\(471785:[^,]+,\(484347:[^,]+,484343:" />
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99 </assert_contents>
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100 </output>
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101 </test>
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102 <test>
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103 <param name="input_alignment" value="sample_aln2.fasta" ftype="fasta" />
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104 <param name="advanced_options_selector" value="false" />
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105 <output name="output_tree">
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106 <assert_contents>
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107 <has_text_matching expression="^\(\(N3970:\d\.\d+,N3339:\d\.\d+\)\d+\.\d+:\d\.\d+,\(\(\(\(N3243:\d\.\d+,\(\(N3234:\d\.\d+,\(N500:" />
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108 </assert_contents>
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109 </output>
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110 </test>
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111 <test>
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112 <param name="input_alignment" value="sample_aln2.fasta" ftype="fasta" />
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113 <param name="advanced_options_selector" value="true" />
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114 <param name="log" value="True" />
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115 <output name="output_log">
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116 <assert_contents>
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117 <has_text text="Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000" />
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118 </assert_contents>
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119 </output>
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120 </test>
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121 </tests>
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122
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123 <help>
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124 <![CDATA[
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125 FastTree infers approximately-maximum-likelihood phylogenetic trees from
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126 alignments of nucleotide or protein sequences. For more information see
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127 the `FastTree`_ website.
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128
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129 .. _FastTree: http://www.microbesonline.org/fasttree
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130 ]]>
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131 </help>
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132
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133 <citations>
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134 <citation type="doi">10.1093/molbev/msp077</citation>
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135 <citation type="doi">10.1371/journal.pone.0009490</citation>
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136 </citations>
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137 </tool>