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annotate pick_open_reference_otus.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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1 <tool id="pick_open_reference_otus" name="Perform open-reference OTU picking"
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2 version="1.9.1">
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3
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4 <description></description>
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5
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9
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10 <expand macro="requirements" />
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12 <version_command><![CDATA[
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13 pick_open_reference_otus.py --version
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14 ]]></version_command>
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16 <command><![CDATA[
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17 pick_open_reference_otus.py
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18
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19 -i $input_seq_files
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21 -o otus
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23 -m $otu_picking_method
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24
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25 #if str( $reference_sequences.reference_sequences_selector ) == 'history'
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26 #set $ref = $reference_sequences.history_database
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27 #else:
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28 #set $data_table = dict([(_[0], _[2]) for _ in $reference_sequences.cached_database.input.options.tool_data_table.data])
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29 #set $db = $reference_sequences.cached_database.value
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30 #set $ref = $data_table[$db]
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31 #end if
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32 -r $ref
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33
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34 #if $prefilter_refseqs_fp.difference_test
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35 #if str( $prefilter_refseqs_fp.prefilter_reference_sequences.reference_sequences_selector ) == 'history'
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36 #set $ref = $prefilter_refseqs_fp.prefilter_reference_sequences.history_database
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37 #else:
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38 #set $data_table = dict([(_[0], _[2]) for _ in $prefilter_refseqs_fp.prefilter_reference_sequences.cached_database.input.options.tool_data_table.data])
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39 #set $db = $prefilter_refseqs_fp.prefilter_reference_sequences.cached_database.value
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40 #set $ref = $data_table[$db]
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41 #end if
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42 --prefilter_refseqs_fp $ref
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43 #end if
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44
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45 -n $new_ref_set_id
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46
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47 $parallel
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48 -O "\${GALAXY_SLOTS:-4}"
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49
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50 -s $percent_subsample
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51 --prefilter_percent_id $prefilter_percent_id
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52
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53 #if str($step1_otu_map_fp) != 'None':
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54 --step1_otu_map_fp $step1_otu_map_fp
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55 #end if
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56
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57 #if str($step1_failures_fasta_fp) != 'None':
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58 --step1_failures_fasta_fp=$step1_failures_fasta_fp
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59 #end if
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60
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61 --minimum_failure_threshold $minimum_failure_threshold
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62
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63 $suppress_step4
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64
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65 --min_otu_size $min_otu_size
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66
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67 $suppress_taxonomy_assignment
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68 $suppress_align_and_tree
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69
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70 &&
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71
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72 biom convert
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73 -i otus/otu_table_mc2.biom
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74 -o $output_otu_table
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75 --to-tsv
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76 --header-key taxonomy
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77
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78 #if not $suppress_taxonomy_assignment
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79 &&
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80 biom convert
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81 -i otus/otu_table_mc2_w_tax.biom
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82 -o $output_otu_table_taxonomy
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83 --to-tsv
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84 --header-key taxonomy
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85 #end if
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86
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87 #if not $suppress_align_and_tree
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88 &&
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89 biom convert
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90 -i otus/otu_table_mc_no_pynast_failures.biom
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91 -o $output_otu_table_no_failures
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92 --to-tsv
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93 --header-key taxonomy
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94 #end if
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95
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96 ]]>
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97 </command>
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98
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99 <inputs>
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100 <param name="input_seq_files" type="data" format="fasta,fastq"
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101 label="Input sequence files" multiple="True" help="(-i/--input_fps)"/>
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102
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103 <param name="otu_picking_method" label="The OTU picking method to use for
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104 reference and de novo steps" type="select"
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105 help="-m/--otu_picking_method">
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106 <option value="uclust" selected="True">uclust</option>
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107 <option value="usearch61">usearch61</option>
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108 <option value="sortmerna_sumaclust">sortmerna_sumaclust</option>
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109 </param>
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110
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111 <conditional name="reference_sequences">
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112 <param name="reference_sequences_selector" type="select"
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113 label="Reference sequences to query"
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114 help="(-r, --reference_fp)">
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115 <option value="cached" selected="True">Public databases</option>
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116 <option value="history">Databases from your history</option>
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117 </param>
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118 <when value="cached">
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119 <param name="cached_database" label="QIIME databases of reference
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120 sequences" type="select">
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121 <options from_data_table="qiime_reference_db" />
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122 </param>
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123 </when>
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124 <when value="history">
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125 <param name="history_database" type="data" format="fasta"
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126 label="Reference databases"/>
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127 </when>
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128 </conditional>
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129
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130 <conditional name="prefilter_refseqs_fp">
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131 <param name="difference_test" type="boolean" label="Use different
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132 reference sequences for the prefilter?" checked="False" truevalue="true"
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133 falsevalue="false" help="(--prefilter_refseqs_fp)" />
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134 <when value="true">
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135 <conditional name="prefilter_reference_sequences">
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136 <param name="reference_sequences_selector" type="select"
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137 label="Reference sequences to query" >
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138 <option value="cached" selected="True">Public databases</option>
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139 <option value="history">Databases from your history</option>
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140 </param>
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141 <when value="cached">
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142 <param name="cached_database" label="QIIME databases of reference
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143 sequences" type="select">
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144 <options from_data_table="qiime_reference_db" />
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145 </param>
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146 </when>
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147 <when value="history">
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148 <param name="history_database" type="data" format="fasta"
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149 label="Reference databases"/>
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150 </when>
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151 </conditional>
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152 </when>
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153 <when value="false" />
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154 </conditional>
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155
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156 <param name="new_ref_set_id" type="text" value="New" label="Unique
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157 identifier for OTUs that get created in this ref set"
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158 help="This is useful to support combining of reference sets
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159 (-n/--new_ref_set_id)"/>
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160
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161 <param name="parallel" type="boolean" label="Run in parallel where
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162 available?" truevalue="--parallel" falsevalue="" checked="False"
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163 help="(-a, --parallel)" />
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164
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165 <param name="percent_subsample" type="float" value="0.001" min="0" max="1"
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166 label="Percent of failure sequences to include in the subsample to
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167 cluster de novo" help="Large numbers should give more comprehensive
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168 results but will be slower(-s/--percent_subsample)"/>
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169
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170 <param name="prefilter_percent_id" type="float" value="0.0" min="0" max="1"
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171 label="Percent of sequence pre-cluster against the reference"
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172 help="Any reads which fail to hit are discarded (a quality filter)
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173 (--prefilter_percent_id)"/>
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174
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175 <param name="step1_otu_map_fp" type="data" format="txt" label="Reference
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176 OTU picking OTU map to avoid rebuilding if one has already been built
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177 (optional)" optional="True" help="This must be an OTU map generated
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178 by this workflow, not (for example) by pick_closed_reference_otus
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179 (--step1_otu_map_fp)" />
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180
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181 <param name="step1_failures_fasta_fp" type="data" format="fasta"
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182 label="Reference OTU picking failures fasta filepath, to avoid
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183 rebuilding if one has already been built (optional)" optional="True"
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184 help="This must be a failures file generated by this workflow, not
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185 (for example) by pick_closed_reference_otus (--step1_failures_fasta_fp)" />
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186
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187 <param name="minimum_failure_threshold" type="integer" value="100000"
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188 label="Minimum number of sequences that must fail to hit the reference
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189 for subsampling to be performed" help="If fewer than this number of
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190 sequences fail to hit the reference, the de novo clustering step will
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191 run serially rather than invoking the subsampled open reference approach
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192 to improve performance (--minimum_failure_threshold)"/>
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193
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194 <param name="suppress_step4" type="boolean" label="Suppress the final de
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195 novo OTU picking step?" truevalue="--suppress_step4" falsevalue=""
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196 checked="False" help="It may be necessary for extremely large data
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197 sets(--suppress_step4)" />
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198
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199 <param name="min_otu_size" type="integer" value="2" label="Minimum otu
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200 size to retain the OTU" help="(--min_otu_size)"/>
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201
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202 <param name="suppress_taxonomy_assignment" type="boolean"
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203 label="Skip the taxonomy assignment step?"
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204 truevalue="--suppress_taxonomy_assignment" falsevalue=""
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205 checked="False" help="It results in an OTU table without taxonomy
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206 (--suppress_taxonomy_assignment)" />
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207
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208 <param name="suppress_align_and_tree" type="boolean"
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209 label="Skip the sequence alignment and tree-building steps?"
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210 truevalue="--suppress_align_and_tree" falsevalue=""
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211 checked="False" help="(--suppress_align_and_tree)" />
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212 </inputs>
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213
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214 <outputs>
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215 <data name="output_rep_set" format="fasta"
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216 from_work_dir="otus/rep_set.fna"
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217 label="${tool.name} on ${on_string}: OTU representative sequences"/>
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218 <data name="output_ref_set" format="fasta"
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219 from_work_dir="otus/new_refseqs.fna"
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220 label="${tool.name} on ${on_string}: New reference sequences (OTU +
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221 input reference sequences)"/>
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222 <data name="output_otu_table" format="tsv"
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223 label="${tool.name} on ${on_string}: OTU table"/>
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224 <data name="output_otu_table_taxonomy" format="tsv"
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225 label="${tool.name} on ${on_string}: OTU table with taxonomy">
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226 <filter>suppress_taxonomy_assignment is False</filter>
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227 </data>
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228 <data name="output_otu_table_no_failures" format="tsv"
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229 label="${tool.name} on ${on_string}: OTU without sequences that
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230 failed to align">
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231 <filter>suppress_align_and_tree is False</filter>
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232 </data>
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233 <data name="output_otu_map" format="txt"
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234 from_work_dir="otus/final_otu_map_mc2.txt"
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235 label="${tool.name} on ${on_string}: OTU map"/>
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236 <data name="output_rep_set_tree" format="txt"
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237 from_work_dir="otus/rep_set.tre"
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238 label="${tool.name} on ${on_string}: representative set tree">
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239 <filter>suppress_align_and_tree is False</filter>
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240 </data>
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241 </outputs>
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242
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243 <tests>
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244 <test>
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245 <param name="input_seq_files"
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246 value="split_fastq_libraries_sequences.fasta"/>
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247 <param name="otu_picking_method" value="uclust"/>
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248 <param name="reference_sequences_selector" value="history"/>
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249 <param name="history_database" value="gg_13_8_97_otus.fasta"/>
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250 <param name="difference_test" value="false"/>
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251 <param name="new_ref_set_id" value="New" />
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252 <param name="parallel" value="--parallel"/>
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253 <param name="percent_subsample" value="0.001" />
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254 <param name="prefilter_percent_id" value="0.0" />
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255 <param name="minimum_failure_threshold" value="100000" />
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256 <param name="suppress_step4" value=""/>
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257 <param name="min_otu_size" value="2" />
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258 <param name="suppress_taxonomy_assignment" value="" />
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259 <param name="suppress_align_and_tree" value="" />
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260
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261 <output name="output_rep_set"
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262 value="pick_open_reference_otus_representative_sequences.fasta"/>
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263 <output name="output_ref_set"
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264 value="pick_open_reference_otus_reference_sequences.fasta"/>
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265 <output name="output_otu_table"
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266 value="pick_open_reference_otus_otu_table.txt"/>
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267 <output name="output_otu_table_taxonomy"
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268 value="pick_open_reference_otus_otu_table_with_taxo.txt" />
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269 <output name="output_otu_map"
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270 value="pick_open_reference_otus_otu_map.txt"/>
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271 <output name="output_otu_table_no_failures"
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272 value="pick_open_reference_otus_otu_table_with_taxo_without_pynast_failure.txt" />
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273 <output name="output_rep_set_tree"
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274 value="pick_open_reference_otus_representative_set_tree.txt" />
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275 </test>
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276 </tests>
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277
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278 <help><![CDATA[
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279
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280 **What it does**
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281
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282 This tool performs open-reference OTU picking from sequences.
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283
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284 This script is broken down into 4 possible OTU picking steps, and 2 steps
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285 involving the creation of OTU tables and trees.
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286
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287 More information about this tool is available on
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288 `QIIME documentation <http://qiime.org/scripts/pick_open_reference_otus.html>`_.
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289 ]]>
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290 </help>
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291
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292 <citations>
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293 <expand macro="citations" />
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294 </citations>
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295 </tool>