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annotate metaphlan2.xml @ 28:1d993cca38e3 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit b467108d731001d89920aee31433a5b0a623c251-dirty
author bebatut
date Thu, 28 Apr 2016 07:04:50 -0400
parents fb2dc25a832d
children 713a83023626
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1 <tool id="metaphlan2" name="MetaPhlAn2" version="2.5.0">
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3 <description>to profile the composition of microbial communities</description>
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5 <macros>
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6 <import>metaphlan2_macros.xml</import>
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7 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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12 <version_command>
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13 <![CDATA[
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14 metaphlan2.py -v
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15 ]]>
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16 </version_command>
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18 <command>
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19 <![CDATA[
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20 (which bowtie2 || exit 200)
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22 &&
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24 metaphlan2.py
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25 $input_file
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26 -o $output_file
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28 --input_type ${input_file.datatype.file_ext}
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30 #if $mpa_pkl.mpa_pkl_selector == "cached"
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31 #set $mpa_pkl_table = dict([(_[0], _[2]) for _ in $mpa_pkl.cached_mpa_pkl.input.options.tool_data_table.data])
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32 #set $mpa_pkl_db = $mpa_pkl.cached_mpa_pkl.value
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33 --mpa_pkl $mpa_pkl_table[$mpa_pkl_db]
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34 #else
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35 --mpa_pkl $mpa_pkl.history_mpa_pkl
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36 #end if
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38 --bowtie2_exe `which bowtie2`
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39
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40 #if $bowtie2db.bowtie2db_selector == "cached"
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41 #set $bowtie2_table = dict([(_[0], _[2]) for _ in $bowtie2db.cached_bowtie2db.input.options.tool_data_table.data])
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42 #set $bowtie2db_choice = $bowtie2db.cached_bowtie2db.value
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43 --bowtie2db $bowtie2_table[$bowtie2db_choice]
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44 #else
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45 --bowtie2db $bowtie2db.history_bowtie2db
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46 #end if
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48 --no_map
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50 -t $analysis_type.analysis_type_select
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51 #if $analysis_type.analysis_type_select == "rel_ab"
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52 --tax_lev $analysis_type.taxonomic_level
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53 #else if $analysis_type.analysis_type_select == "marker_ab_table"
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54 --nreads $analysis_type.nreads
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55 #else if $analysis_type.analysis_type_select == "marker_pres_table"
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56 --pres_th $analysis_type.pres_th
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57 #end if
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58
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59 --min_cu_len $min_cu_len
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60 --min_alignment_len $min_alignment_len
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62 $ignore_viruses
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63 $ignore_eukaryotes
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64 $ignore_bacteria
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65 $ignore_archaea
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66
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67 --stat_q $stat_q
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68
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69 #if $sam_output
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70 -s $sam_output_file
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71 #end if
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73 #if $biom_output
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74 --biom $biom_output_file
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75 #end if
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76 ]]>
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77 </command>
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79 <inputs>
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80 <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/>
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81
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82 <conditional name="mpa_pkl">
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83 <param name="mpa_pkl_selector" type="select" label="Metadata" help="">
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84 <option value="cached" selected="true">Locally cached</option>
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85 <option value="history">From history</option>
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86 </param>
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87
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88 <when value="cached">
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89 <param name="cached_mpa_pkl" label="Cached metadata" type="select">
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90 <options from_data_table="metaphlan2_metadata" />
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91 </param>
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92 </when>
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93 <when value="history">
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94 <param name="history_mpa_pkl" type="data" format="fasta" label="Metadata from history"/>
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95 </when>
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96 </conditional>
27
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97
28
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98 <conditional name="bowtie2db">
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99 <param name="bowtie2db_selector" type="select" label="BowTie2 database" help="">
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100 <option value="cached" selected="true">Locally cached</option>
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101 <option value="history">From history</option>
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102 </param>
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103
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104 <when value="cached">
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105 <param name="cached_bowtie2db" label="Cached BowTie2 database" type="select" >
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106 <options from_data_table="metaphlan2_bowtie_db" />
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107 </param>
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108 </when>
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109 <when value="history">
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110 <param name="history_bowtie2db" type="data" format="fasta" label="BowTie2 database from history"/>
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111 </when>
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112 </conditional>
27
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113
0
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114 <conditional name="analysis_type">
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115 <param name="analysis_type_select" type="select" label="Type of analysis to perform">
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116 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
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117 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
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118 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
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119 <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option>
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120 <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option>
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121 <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
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122 </param>
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123
0
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124 <when value="rel_ab">
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125 <param name="taxonomic_level" type="select" label="Taxonomic level for the relative abundance output">
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126 <option value="a" selected="true">All taxonomic levels</option>
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127 <option value="k">Kingdoms (Bacteria and Archaea) only</option>
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128 <option value="p">Phyla only</option>
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129 <option value="c">Classes only</option>
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130 <option value="o">Orders only</option>
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131 <option value="f">Families only</option>
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132 <option value="g">Genera only</option>
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133 <option value="s">Species only</option>
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134 </param>
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135 </when>
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136
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137 <when value="reads_map"/>
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138 <when value="clade_profiles"/>
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139
0
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140 <when value="marker_ab_table">
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141 <param name="nreads" type="integer" value="0" label="Total number of reads in the original metagenome" help="It is used for normalizing the length-normalized counts with the metagenome size as well. No normalization applied if the value is not specified"/>
0
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142 </when>
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143
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144 <when value="marker_counts"/>
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145
0
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146 <when value="marker_pres_table">
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147 <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/>
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148 </when>
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149 </conditional>
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150
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151 <param name="min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances" help=""/>
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152
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153 <param name="min_alignment_len" type="integer" value="0" label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded." help=""/>
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154
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155 <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" />
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156 <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" />
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157
0
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158 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" />
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159
0
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160 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />
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161
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162 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
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163
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164 <param name="sam_output" type='boolean' label="Output a sam file?" help="" />
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165
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166 <param name="biom_output" type='boolean' label="Output a biom file?" help="" />
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167 </inputs>
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168
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169 <outputs>
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170 <data format="tabular" name="output_file"
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171 metadata="input_sequence_file"
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172 label="${tool.name} on ${on_string}: Community profile" />
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173
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174 <data format="sam" name="sam_output_file"
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175 metadata="input_sequence_file"
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176 label="${tool.name} on ${on_string}: Sam file">
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177 <filter>sam_output</filter>
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178 </data>
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179 <data format="biom" name="biom_output_file"
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180 metadata="input_sequence_file"
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181 label="${tool.name} on ${on_string}: Biom file">
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182 <filter>biom_output</filter>
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183 </data>
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184 </outputs>
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185
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186 <tests>
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187 <test>
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188 <param name="input_file" value="metaphlan2_input_sequences.fastq"/>
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189 <param name="mpa_pkl" value="" />
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190 <param name="bowtie2db" value="" />
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191 <param name="analysis_type_select" value="rel_ab" />
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192 <param name="taxonomic_level" value="a" />
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193 <param name="min_cu_len" value="2000" />
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194 <param name="min_alignment_len" value="0" />
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195 <param name="ignore_viruses" value="" />
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196 <param name="ignore_eukaryotes" value="" />
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197 <param name="ignore_bacteria" value="" />
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198 <param name="ignore_archaea" value="" />
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199 <param name="stat_q" value="0.1" />
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200 <param name="sam_output" value='false' />
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201 <param name="biom_output" value='false' />
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202 <output name="output_file" file="metaphlan2_profiled_metagenome.txt"/>
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203 </test>
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204 </tests>
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205
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206 <help><![CDATA[
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207
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208 **What it does**
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209
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210 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
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211
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212 Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced
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213 SAM file or an intermediary mapping file of the metagenome generated by a
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214 previous MetaPhlAn
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215
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216 Several parameters can modulate the MetaPhlAn execution
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217
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218 * Mapping arguments
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219
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220 * Test to avoid saving the output of BowTie2
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221
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222 * Post-mapping arguments
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223
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224 * Taxonomic level for the relative abundance output
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225 * Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances
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226 * Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded
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227 * Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea
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228 * Quantile value
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229
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230 * Additional analysis types and arguments
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231
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232 * Type of analyse to perform and some parameters for specific analysis type
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233
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234
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235 The main output file is a tab-separated output file of the predicted taxon
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236 relative abundances.
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237
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238 ]]></help>
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239
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240 <citations>
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241 <citation type="doi">10.1038/nmeth.3589</citation>
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242 </citations>
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243 </tool>