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comparison metaphlan2.xml @ 0:8b151cff43e0 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 89a1d80e981c147c87c892384afd8411dccfd8a1-dirty
author bebatut
date Thu, 17 Dec 2015 04:03:29 -0500
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1 <tool id="metaphlan_2" name="MetaPhlAn2" version="0.1.0">
2
3 <description>to profile the composition of microbial communities</description>
4
5 <requirements>
6 <requirement type="package" version="2.2.5">bowtie2</requirement>
7 <requirement type="package" version="2.0">metaphlan2</requirement>
8 </requirements>
9
10 <stdio>
11 <exit_code range="1:" level="fatal" description="" />
12 <regex match="ERROR"
13 source="stderr"
14 level="fatal"
15 description="" />
16 <regex match="WARNING"
17 source="stderr"
18 level="warning"
19 description="" />
20 </stdio>
21
22 <version_command>
23 <![CDATA[
24 python \${METAPHLAN2_DIR}/metaphlan2.py -v
25 ]]>
26 </version_command>
27
28 <command>
29 <![CDATA[
30 (which bowtie2 || exit 200)
31
32 &&
33
34 python \${METAPHLAN2_DIR}/metaphlan2.py
35 $input_file
36 -o $output_file
37
38 --input_type ${input_file.datatype.file_ext}
39 --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl
40
41 --bowtie2_exe `which bowtie2`
42 --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200
43
44 --no_map
45
46 -t $analysis_type.analysis_type_select
47 #if $analysis_type.analysis_type_select == "rel_ab"
48 --tax_lev $analysis_type.taxonomic_level
49 #else if $analysis_type.analysis_type_select == "marker_ab_table"
50 --nreads $analysis_type.nreads
51 #else if $analysis_type.analysis_type_select == "marker_pres_table"
52 --pres_th $analysis_type.pres_th
53 #end if
54
55 --min_cu_len $min_cu_len
56 --min_alignment_len $min_alignment_len
57
58 $ignore_viruses
59 $ignore_eukaryotes
60 $ignore_bacteria
61 $ignore_archaea
62
63 --stat_q $stat_q
64
65 #if $sam_output
66 -s $sam_output_file
67 #end if
68
69 #if $biom_output
70 --biom $biom_output_file
71 #end if
72 ]]>
73 </command>
74
75 <inputs>
76 <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/>
77
78 <conditional name="analysis_type">
79 <param name="analysis_type_select" type="select" label="Type of analysis to perform">
80 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
81 <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>
82 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
83 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
84 <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option>
85 <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
86 </param>
87 <when value="rel_ab">
88 <param name="taxonomic_level" type="select" label="Taxonomic level for the relative abundance output">
89 <option value="a" selected="true">All taxonomic levels</option>
90 <option value="k">Kingdoms (Bacteria and Archaea) only</option>
91 <option value="p">Phyla only</option>
92 <option value="c">Classes only</option>
93 <option value="o">Orders only</option>
94 <option value="f">Families only</option>
95 <option value="g">Genera only</option>
96 <option value="s">Species only</option>
97 </param>
98 </when>
99 <when value="rel_ab_w_read_stats"/>
100 <when value="reads_map"/>
101 <when value="clade_profiles"/>
102 <when value="marker_ab_table">
103 <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"/>
104 </when>
105 <when value="marker_pres_table">
106 <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/>
107 </when>
108 </conditional>
109
110 <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=""/>
111
112 <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=""/>
113
114 <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" />
115 <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" />
116 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" />
117 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />
118
119 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
120
121 <param name="sam_output" type='boolean' label="Output a sam file?" help="" />
122 <param name="biom_output" type='boolean' label="Output a biom file?" help="" />
123 </inputs>
124
125 <outputs>
126 <data format="txt" name="output_file"
127 metadata="input_sequence_file"
128 label="Profile of communities on ${on_string} (MetaPhlAn)" />
129
130 <data format="sam" name="sam_output_file"
131 metadata="input_sequence_file"
132 label="Sam output on ${on_string} (MetaPhlAn)">
133 <filter>sam_output</filter>
134 </data>
135 <data format="biom" name="biom_output_file"
136 metadata="input_sequence_file"
137 label="Biom output on ${on_string} (MetaPhlAn)">
138 <filter>biom_output</filter>
139 </data>
140 </outputs>
141
142 <tests>
143 <test>
144 <param name="input_file" value="metaphlan2_input_sequences.fastq"/>
145 <param name="analysis_type_select" value="rel_ab" />
146 <param name="taxonomic_level" value="a" />
147 <param name="min_cu_len" value="2000" />
148 <param name="min_alignment_len" value="0" />
149 <param name="ignore_viruses" value="" />
150 <param name="ignore_eukaryotes" value="" />
151 <param name="ignore_bacteria" value="" />
152 <param name="ignore_archaea" value="" />
153 <param name="stat_q" value="0.1" />
154 <param name="sam_output" value='false' />
155 <param name="biom_output" value='true' />
156 <output name="output_file" file="metaphlan2_profiled_metagenome.txt"/>
157 <output name="biom_output_file" file="metaphlan2_biom.biom"/>
158 </test>
159 </tests>
160
161 <help><![CDATA[
162
163 **What it does**
164
165 MetaPhlAn is a computational tool for profiling the composition of microbial
166 communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun
167 sequencing data with species level resolution. For more information, check the
168 `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
169
170 -----
171
172 **Input**
173
174 Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced
175 SAM file or an intermediary mapping file of the metagenome generated by a
176 previous MetaPhlAn
177
178 -----
179
180 **Parameters**
181
182 Several parameters can modulate the MetaPhlAn execution
183
184 * Mapping arguments
185
186 * Test to avoid saving the output of BowTie2
187
188 * Post-mapping arguments
189
190 * Taxonomic level for the relative abundance output
191 * Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances
192 * Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded
193 * Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea
194 * Quantile value
195
196 * Additional analysis types and arguments
197
198 * Type of analyse to perform and some parameters for specific analysis type
199
200 -----
201
202 **Outputs**
203
204 The main output file is a tab-separated output file of the predicted taxon
205 relative abundances.
206
207 Given the choosen parameters, other output files can be:
208
209 * a sam output file
210 * a biom output fime
211 * a BowTie2 output file
212
213 ]]></help>
214
215 <citations>
216 <citation type="doi">10.1038/nmeth.3589</citation>
217 </citations>
218 </tool>