Mercurial > repos > bebatut > metaphlan2

annotate metaphlan2.xml @ 27:fb2dc25a832d draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
author bebatut
date Tue, 12 Apr 2016 03:07:32 -0400
parents 3f52f2d65d41
children 1d993cca38e3
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1 <tool id="metaphlan2" name="MetaPhlAn2" version="2.2.0">
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3 <description>to profile the composition of microbial communities</description>
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5 <requirements>
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6 <requirement type="package" version="2.2.5">bowtie2</requirement>
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7 <requirement type="package" version="2.2.0">metaphlan2</requirement>
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8 </requirements>
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10 <stdio>
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11 <exit_code range="1:" level="fatal" description="" />
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12 <regex match="ERROR"
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13 source="stderr"
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14 level="fatal"
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15 description="" />
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16 <regex match="WARNING"
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17 source="stderr"
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18 level="warning"
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19 description="" />
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20 </stdio>
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22 <version_command>
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23 <![CDATA[
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24 metaphlan2.py -v
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25 ]]>
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26 </version_command>
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28 <command>
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29 <![CDATA[
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30 (which bowtie2 || exit 200)
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32 &&
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34 metaphlan2.py
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35 $input_file
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36 -o $output_file
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38 --input_type ${input_file.datatype.file_ext}
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40 #set $data_table = dict([(_[0], _[2]) for _ in $mpa_pkl.input.options.tool_data_table.data])
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41 #set $db = $mpa_pkl.value
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42 --mpa_pkl $data_table[$db]
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44 --bowtie2_exe `which bowtie2`
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46 #set $data_table = dict([(_[0], _[2]) for _ in $bowtie2db.input.options.tool_data_table.data])
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47 #set $db = $bowtie2db.value
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48 --bowtie2db $data_table[$db]
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49
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50 --no_map
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52 -t $analysis_type.analysis_type_select
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53 #if $analysis_type.analysis_type_select == "rel_ab"
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54 --tax_lev $analysis_type.taxonomic_level
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55 #else if $analysis_type.analysis_type_select == "marker_ab_table"
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56 --nreads $analysis_type.nreads
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57 #else if $analysis_type.analysis_type_select == "marker_pres_table"
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58 --pres_th $analysis_type.pres_th
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59 #end if
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61 --min_cu_len $min_cu_len
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62 --min_alignment_len $min_alignment_len
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64 $ignore_viruses
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65 $ignore_eukaryotes
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66 $ignore_bacteria
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67 $ignore_archaea
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68
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69 --stat_q $stat_q
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70
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71 #if $sam_output
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72 -s $sam_output_file
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73 #end if
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75 #if $biom_output
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76 --biom $biom_output_file
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77 #end if
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78 ]]>
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79 </command>
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81 <inputs>
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82 <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/>
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83
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84 <param name="mpa_pkl" label="Metadata" type="select" >
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85 <options from_data_table="metaphlan2_metadata" />
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86 </param>
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87
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88 <param name="bowtie2db" label="BowTie2 database" type="select" >
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89 <options from_data_table="metaphlan2_bowtie_db" />
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90 </param>
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91
0
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92 <conditional name="analysis_type">
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93 <param name="analysis_type_select" type="select" label="Type of analysis to perform">
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94 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
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95 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
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96 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
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97 <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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98 <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option>
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99 <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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100 </param>
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101 <when value="rel_ab">
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102 <param name="taxonomic_level" type="select" label="Taxonomic level for the relative abundance output">
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103 <option value="a" selected="true">All taxonomic levels</option>
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104 <option value="k">Kingdoms (Bacteria and Archaea) only</option>
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105 <option value="p">Phyla only</option>
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106 <option value="c">Classes only</option>
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107 <option value="o">Orders only</option>
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108 <option value="f">Families only</option>
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109 <option value="g">Genera only</option>
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110 <option value="s">Species only</option>
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111 </param>
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112 </when>
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113 <when value="reads_map"/>
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114 <when value="clade_profiles"/>
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115 <when value="marker_ab_table">
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116 <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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117 </when>
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118 <when value="marker_counts"/>
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119 <when value="marker_pres_table">
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120 <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/>
0
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121 </when>
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122 </conditional>
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123
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124 <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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125
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126 <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=""/>
0
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127
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128 <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" />
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129 <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" />
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130 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" />
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131 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />
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132
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133 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
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134
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135 <param name="sam_output" type='boolean' label="Output a sam file?" help="" />
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136 <param name="biom_output" type='boolean' label="Output a biom file?" help="" />
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137 </inputs>
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138
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139 <outputs>
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140 <data format="tabular" name="output_file"
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141 metadata="input_sequence_file"
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142 label="Profile of communities on ${on_string} (MetaPhlAn)" />
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143
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144 <data format="sam" name="sam_output_file"
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145 metadata="input_sequence_file"
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146 label="Sam output on ${on_string} (MetaPhlAn)">
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147 <filter>sam_output</filter>
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148 </data>
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149 <data format="biom" name="biom_output_file"
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150 metadata="input_sequence_file"
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151 label="Biom output on ${on_string} (MetaPhlAn)">
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152 <filter>biom_output</filter>
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153 </data>
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154 </outputs>
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155
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156 <tests>
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157 <test>
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158 <param name="input_file" value="metaphlan2_input_sequences.fastq"/>
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159 <param name="mpa_pkl" value="" />
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160 <param name="bowtie2db" value="" />
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161 <param name="analysis_type_select" value="rel_ab" />
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162 <param name="taxonomic_level" value="a" />
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163 <param name="min_cu_len" value="2000" />
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164 <param name="min_alignment_len" value="0" />
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165 <param name="ignore_viruses" value="" />
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166 <param name="ignore_eukaryotes" value="" />
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167 <param name="ignore_bacteria" value="" />
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168 <param name="ignore_archaea" value="" />
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169 <param name="stat_q" value="0.1" />
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170 <param name="sam_output" value='false' />
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171 <param name="biom_output" value='false' />
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172 <output name="output_file" file="metaphlan2_profiled_metagenome.txt"/>
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173 </test>
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174 </tests>
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175
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176 <help><![CDATA[
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177
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178 **What it does**
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179
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180 MetaPhlAn is a computational tool for profiling the composition of microbial
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181 communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun
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182 sequencing data with species level resolution. For more information, check the
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183 `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
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184
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185 -----
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186
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187 **Input**
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188
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189 Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced
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190 SAM file or an intermediary mapping file of the metagenome generated by a
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191 previous MetaPhlAn
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192
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193 -----
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194
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195 **Parameters**
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196
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197 Several parameters can modulate the MetaPhlAn execution
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198
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199 * Mapping arguments
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200
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201 * Test to avoid saving the output of BowTie2
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202
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203 * Post-mapping arguments
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204
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205 * Taxonomic level for the relative abundance output
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206 * Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances
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207 * Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded
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208 * Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea
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209 * Quantile value
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210
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211 * Additional analysis types and arguments
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212
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213 * Type of analyse to perform and some parameters for specific analysis type
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214
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215 -----
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216
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217 **Outputs**
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218
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219 The main output file is a tab-separated output file of the predicted taxon
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220 relative abundances.
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221
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222 Given the choosen parameters, other output files can be:
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223
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224 * a sam output file
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225 * a biom output fime
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226 * a BowTie2 output file
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227
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228 ]]></help>
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229
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230 <citations>
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231 <citation type="doi">10.1038/nmeth.3589</citation>
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232 </citations>
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233 </tool>