Mercurial > repos > iuc > qiime_make_phylogeny

annotate make_phylogeny.xml @ 0:e82369a926e3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:34:15 -0400
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children 9e5b2251a6a5
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0
e82369a926e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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1 <tool id="qiime_make_phylogeny" name="Make phylogeny" version="@WRAPPER_VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="8.2.9">raxml</requirement>
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8 <requirement type="package" version="2.1">clustalw</requirement>
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9 <requirement type="package" version="3.8.1551">muscle</requirement>
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10 <requirement type="package" version="1.0.9">clearcut</requirement>
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11 </expand>
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12 <version_command>make_phylogeny.py --version</version_command>
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13 <command detect_errors="aggressive"><![CDATA[
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14 make_phylogeny.py
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15 --input_fp '$input_fp'
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16 --result_fp '$result_fp'
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17 --tree_method '$tree_method'
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18 --log_fp '$log_fp'
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19 --root_method '$root_method'
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20 ]]></command>
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21 <inputs>
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22 <param argument="--input_fp" type="data" format="fasta" label="Input fasta alignment"/>
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23 <param argument="--tree_method" type="select" label="Method for tree building">
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24 <option value="clustalw">ClustalW</option>
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25 <option value="raxml_v730">raxml_v730</option>
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26 <option value="muscle">muscle</option>
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27 <option value="fasttree" selected="true">fasttree</option>
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28 <option value="clearcut">clearcut</option>
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29 </param>
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30 <param argument="--root_method" type="select" label="Method for choosing root of phylo tree">
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31 <option value="midpoint">Midpoint</option>
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32 <option value="tree_method_default" selected="true">Default method of tree method</option>
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33 </param>
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34 </inputs>
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35 <outputs>
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36 <data name="result_fp" format="nhx" label="${tool.name} on ${on_string}: Tree"/>
e82369a926e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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37 <data name="log_fp" format="txt" label="${tool.name} on ${on_string}: Log"/>
e82369a926e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
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42 <param name="tree_method" value="fasttree"/>
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43 <param name="root_method" value="tree_method_default" />
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44 <output name="result_fp" file="make_phylogeny/fasttree_tree_method_default.tre"/>
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45 <output name="log_fp">
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46 <assert_contents>
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47 <has_text text="Method:fasttree"/>
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48 <has_text text="CogentTreeBuilder parameters:"/>
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49 </assert_contents>
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50 </output>
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51 </test>
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52 <test>
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53 <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
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54 <param name="tree_method" value="raxml_v730"/>
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55 <param name="root_method" value="tree_method_default" />
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56 <output name="result_fp" ftype="nhx" >
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57 <assert_contents>
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58 <has_text text="seq_20"/>
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59 <has_text text="seq_46"/>
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60 <has_text text="seq_11"/>
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61 </assert_contents>
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62 </output>
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63 <output name="log_fp">
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64 <assert_contents>
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65 <has_text text="Method:raxml_v730"/>
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66 <has_text text="CogentTreeBuilder parameters:"/>
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67 </assert_contents>
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68 </output>
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69 </test>
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70 <test>
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71 <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
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72 <param name="tree_method" value="muscle"/>
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73 <param name="root_method" value="tree_method_default" />
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74 <output name="result_fp" file="make_phylogeny/muscle.tre"/>
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75 <output name="log_fp">
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76 <assert_contents>
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77 <has_text text="Method:muscle"/>
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78 <has_text text="CogentTreeBuilder parameters:"/>
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79 </assert_contents>
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80 </output>
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81 </test>
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82 <test>
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83 <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
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84 <param name="tree_method" value="clustalw"/>
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85 <param name="root_method" value="tree_method_default" />
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86 <output name="result_fp" file="make_phylogeny/clustalw.tre"/>
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87 <output name="log_fp">
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88 <assert_contents>
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89 <has_text text="Method:clustalw"/>
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90 <has_text text="CogentTreeBuilder parameters:"/>
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91 </assert_contents>
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92 </output>
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93 </test>
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94 <test>
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95 <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
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96 <param name="tree_method" value="clearcut"/>
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97 <param name="root_method" value="tree_method_default" />
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98 <output name="result_fp" ftype="nhx" >
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99 <assert_contents>
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100 <has_text text="seq_20"/>
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101 <has_text text="seq_46"/>
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102 <has_text text="seq_11"/>
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103 </assert_contents>
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104 </output>
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105 <output name="log_fp">
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106 <assert_contents>
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107 <has_text text="Method:clearcut"/>
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108 <has_text text="CogentTreeBuilder parameters:"/>
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109 </assert_contents>
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110 </output>
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111 </test>
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112 <test>
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113 <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
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114 <param name="tree_method" value="fasttree"/>
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115 <param name="root_method" value="midpoint" />
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116 <output name="result_fp" file="make_phylogeny/fasttree_midpoint.tre"/>
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117 <output name="log_fp">
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118 <assert_contents>
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119 <has_text text="Method:fasttree"/>
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120 <has_text text="CogentTreeBuilder parameters:"/>
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121 </assert_contents>
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122 </output>
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123 </test>
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124 </tests>
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125 <help><![CDATA[
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126 **What it does**
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127
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128 This tool produces a tree from a multiple sequence alignment. Trees are constructed with a set of sequences representative of the OTUs
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129
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130 More information about this tool is available on
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131 `QIIME documentation <http://qiime.org/scripts/make_phylogeny.html>`_.
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132 ]]></help>
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133 <citations>
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134 <expand macro="citations"/>
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135 </citations>
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136 </tool>