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annotate metaphlan2.xml @ 35:c312685a4b26 draft

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author bebatut
date Wed, 22 Feb 2017 09:27:24 -0500
parents 476d18d599c9
children 969ae2fd4c84
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1 <tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.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 <requirement type="package" version="2.2.5">bowtie2</requirement>
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11 </expand>
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13 <expand macro="stdio"/>
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15 <version_command>
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16 <![CDATA[
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17 metaphlan2.py -v
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18 ]]>
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19 </version_command>
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21 <command>
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22 <![CDATA[
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23 (which bowtie2 || exit 200)
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25 &&
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27 #if $db.db_selector == "history"
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28 mkdir ref_db
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29 &&
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30 bowtie2-build '$db.bowtie2db' 'ref_db/ref_db'
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31 &&
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32 python '$__tool_directory__/transform_json_to_pkl.py'
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33 --json_input '$db.mpa_pkl'
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34 --pkl_output 'ref_db/metadata.pkl'
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35 &&
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36 #end if
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38 metaphlan2.py
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39 '$input_file'
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40 -o '$output_file'
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41 --input_type '${input_file.datatype.file_ext}'
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42 --bowtie2_exe `which bowtie2`
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44 #if $db.db_selector == "cached"
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45 #set $paths = dict([(_[0], _[3]) for _ in $db.cached_db.input.options.tool_data_table.data])
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46 #set $db_choice = $db.cached_db.value
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47 --bowtie2db `ls $paths[$db_choice]/*.pkl | sed 's/\(.*\)\..*/\1/'`
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48 --mpa_pkl `ls $paths[$db_choice]/*.pkl`
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49 #else
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50 --bowtie2db 'ref_db/ref_db'
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51 --mpa_pkl 'ref_db/metadata.pkl'
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52 #end if
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54 --no_map
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56 -t '$analysis_type.analysis_type_select'
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57 #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats"
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58 --tax_lev '$analysis_type.taxonomic_level'
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59 #else if $analysis_type.analysis_type_select == "marker_ab_table"
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60 --nreads '$analysis_type.nreads'
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61 #else if $analysis_type.analysis_type_select == "marker_pres_table"
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62 --pres_th '$analysis_type.pres_th'
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63 #end if
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65 --min_cu_len '$min_cu_len'
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66 --min_alignment_len '$min_alignment_len'
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68 $ignore_viruses
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69 $ignore_eukaryotes
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70 $ignore_bacteria
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71 $ignore_archaea
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72
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73 --stat_q '$stat_q'
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74 -s '$sam_output_file'
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75 --biom '$biom_output_file'
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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" label="Input file" help=""/>
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81 <conditional name="db">
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82 <param name="db_selector" type="select" label="Database with clade-specific marker genes" help="">
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83 <option value="cached" selected="true">Locally cached</option>
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84 <option value="history">From history</option>
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85 </param>
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86 <when value="cached">
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87 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" >
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88 <options from_data_table="metaphlan2_database" />
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89 </param>
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90 </when>
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91 <when value="history">
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92 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
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93 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/>
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94 </when>
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95 </conditional>
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96 <conditional name="analysis_type">
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97 <param name="analysis_type_select" type="select" label="Type of analysis to perform" argument="-t">
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98 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
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99 <option value="rel_ab_w_read_stats">Profiling a metagenomes in terms of relative abundances and estimate the number of reads comming from each clade</option>
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100 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
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101 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
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102 <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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103 <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option>
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104 <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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105 </param>
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106 <when value="rel_ab">
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107 <param argument="--taxonomic_level" type="select" label="Taxonomic level for the relative abundance output">
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108 <option value="a" selected="true">All taxonomic levels</option>
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109 <option value="k">Kingdoms (Bacteria and Archaea) only</option>
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110 <option value="p">Phyla only</option>
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111 <option value="c">Classes only</option>
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112 <option value="o">Orders only</option>
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113 <option value="f">Families only</option>
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114 <option value="g">Genera only</option>
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115 <option value="s">Species only</option>
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116 </param>
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117 </when>
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118 <when value="rel_ab_w_read_stats">
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119 <param argument="--taxonomic_level" type="select" label="Taxonomic level for the relative abundance output">
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120 <option value="a" selected="true">All taxonomic levels</option>
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121 <option value="k">Kingdoms (Bacteria and Archaea) only</option>
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122 <option value="p">Phyla only</option>
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123 <option value="c">Classes only</option>
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124 <option value="o">Orders only</option>
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125 <option value="f">Families only</option>
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126 <option value="g">Genera only</option>
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127 <option value="s">Species only</option>
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128 </param>
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129 </when>
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130 <when value="reads_map"/>
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131 <when value="clade_profiles"/>
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132 <when value="marker_ab_table">
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133 <param argument="--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"/>
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134 </when>
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135 <when value="marker_counts"/>
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136 <when value="marker_pres_table">
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137 <param argument="--pres_th" type="integer" value="0" label=" Threshold for calling a marker present"/>
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138 </when>
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139 </conditional>
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140 <param argument="--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"/>
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141 <param argument="--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."/>
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142 <param argument="--ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?"/>
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143 <param argument="--ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?"/>
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144 <param argument="--ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?"/>
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145 <param argument="--ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?"/>
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146 <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/>
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147 <param argument="--sample_id_key" type="text" value="#SampleID" label="Sample ID key"/>
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148 <param argument="--sample_id" type="text" value="Metaphlan2_Analysis" label="Sample ID"/>
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149 </inputs>
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150
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151 <outputs>
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152 <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" />
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153 <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" />
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154 <data format="biom" name="biom_output_file" label="${tool.name} on ${on_string}: BIOM file" />
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155 </outputs>
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156
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157 <tests>
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158 <test>
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159 <param name="input_file" value="input_sequences.fasta"/>
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160 <param name="db_selector" value="history" />
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161 <param name="mpa_pkl" value="marker_metadata.json" />
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162 <param name="bowtie2db" value="marker_sequences.fasta" />
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163 <param name="analysis_type_select" value="rel_ab" />
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164 <param name="taxonomic_level" value="a" />
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165 <param name="min_cu_len" value="2000" />
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166 <param name="min_alignment_len" value="0" />
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167 <param name="ignore_viruses" value="" />
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168 <param name="ignore_eukaryotes" value="" />
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169 <param name="ignore_bacteria" value="" />
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170 <param name="ignore_archaea" value="" />
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171 <param name="stat_q" value="0.1" />
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172 <param name="sample_id_key" value="#SampleID"/>
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173 <param name="sample_id" value="Metaphlan2_Analysis"/>
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174 <output name="output_file" file="community_profile.tabular"/>
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175 </test>
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176 </tests>
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177
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178 <help><![CDATA[
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179 **What it does**
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180
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181 MetaPhlAn is a computational tool to profile the structure and 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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182
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183 **Inputs**
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184
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185 Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced SAM file.
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186
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187 It is also possible to use a custom database with clade-specific marker genes. In this case, a fasta file with marker gene sequences is required and also a file containing metadata. This file is a json file with:
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188
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189 ::
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190
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191 {
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192 "taxonomy": {
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193 "taxonomy of genome1": genome1_length,
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194 "taxonomy of genome2": genome2_length,
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195 ...
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196 }
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197 "markers": {
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198 "marker1_name": {
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199 "clade": the clade that the marker belongs to,
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200 "ext": [list of external genomes where the marker appears],
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201 "len": length of the marker,
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202 "score": score of the marker,
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203 "taxon": the taxon of the marker
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204 }
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205 ...
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206 }
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207 }
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208
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209 The marker name correspond to the corresponding sequence name in the FastA file containing marker gene sequences.
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210
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211 **Outputs**
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212
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213 The main output file is a tab-separated file with the predicted taxon relative abundances.
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214
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215 ]]></help>
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216
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217 <expand macro="citations"/>
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218 </tool>