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comparison metaphlan2.xml @ 31:83f06bee818c draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
author bebatut
date Tue, 21 Feb 2017 12:29:37 -0500
parents 99fe591b59fb
children c941148c75c7
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30:99fe591b59fb 31:83f06bee818c
1 <tool id="metaphlan2" name="MetaPhlAn2" version="2.5.0"> 1 <tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.0">
2 2
3 <description>to profile the composition of microbial communities</description> 3 <description>to profile the composition of microbial communities</description>
4 4
5 <macros> 5 <macros>
6 <import>metaphlan2_macros.xml</import> 6 <import>metaphlan2_macros.xml</import>
7 </macros> 7 </macros>
8 8
9 <expand macro="requirements"/> 9 <expand macro="requirements">
10 <requirement type="package" version="2.2.5">bowtie2</requirement>
11 </expand>
12
10 <expand macro="stdio"/> 13 <expand macro="stdio"/>
11 14
12 <version_command> 15 <version_command>
13 <![CDATA[ 16 <![CDATA[
14 metaphlan2.py -v 17 metaphlan2.py -v
22 && 25 &&
23 26
24 #if $db.db_selector == "history" 27 #if $db.db_selector == "history"
25 mkdir ref_db 28 mkdir ref_db
26 && 29 &&
27 bowtie2-build $db.db_sequences ref_db/ref_db 30 bowtie2-build '$db.bowtie2db' 'ref_db/ref_db'
28 && 31 &&
29 python $__tool_directory__/transform_json_to_pkl.py 32 python '$__tool_directory__/transform_json_to_pkl.py'
30 --json_input $db_metadata 33 --json_input '$db.mpa_pkl'
31 --pkl_output ref_db/metadata.pkl 34 --pkl_output 'ref_db/metadata.pkl'
32 && 35 &&
33 #end if 36 #end if
34 37
35 metaphlan2.py 38 metaphlan2.py
36 $input_file 39 '$input_file'
37 -o $output_file 40 -o '$output_file'
38 --input_type ${input_file.datatype.file_ext} 41 --input_type '${input_file.datatype.file_ext}'
39 42
40 --bowtie2_exe `which bowtie2` 43 --bowtie2_exe `which bowtie2`
41 44
42 #if $db.db_selector == "cached" 45 #if $db.db_selector == "cached"
43 #set $table = dict([(_[0], _[2]) for _ in $db.cached_db.input.options.tool_data_table.data]) 46 #set $table = dict([(_[0], _[2]) for _ in $db.cached_db.input.options.tool_data_table.data])
44 #set $db_choice = $db.cached_db.value 47 #set $db_choice = $db.cached_db.value
45 --bowtie2db $table[$db_choice] 48 --bowtie2db '$table[$db_choice]'
46 --mpa_pkl $table[$db_choice]".pkl" 49 --mpa_pkl $table[$db_choice]".pkl"
47 #else 50 #else
48 --bowtie2db ref_db/ref_db 51 --bowtie2db 'ref_db/ref_db'
49 --mpa_pkl ref_db/metadata.pkl 52 --mpa_pkl 'ref_db/metadata.pkl'
50 #end if 53 #end if
51 54
52 --no_map 55 --no_map
53 56
54 -t $analysis_type.analysis_type_select 57 -t '$analysis_type.analysis_type_select'
55 #if $analysis_type.analysis_type_select == "rel_ab" 58 #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats"
56 --tax_lev $analysis_type.taxonomic_level 59 --tax_lev '$analysis_type.taxonomic_level'
57 #else if $analysis_type.analysis_type_select == "marker_ab_table" 60 #else if $analysis_type.analysis_type_select == "marker_ab_table"
58 --nreads $analysis_type.nreads 61 --nreads '$analysis_type.nreads'
59 #else if $analysis_type.analysis_type_select == "marker_pres_table" 62 #else if $analysis_type.analysis_type_select == "marker_pres_table"
60 --pres_th $analysis_type.pres_th 63 --pres_th '$analysis_type.pres_th'
61 #end if 64 #end if
62 65
63 --min_cu_len $min_cu_len 66 --min_cu_len '$min_cu_len'
64 --min_alignment_len $min_alignment_len 67 --min_alignment_len '$min_alignment_len'
65 68
66 $ignore_viruses 69 $ignore_viruses
67 $ignore_eukaryotes 70 $ignore_eukaryotes
68 $ignore_bacteria 71 $ignore_bacteria
69 $ignore_archaea 72 $ignore_archaea
70 73
71 --stat_q $stat_q 74 --stat_q '$stat_q'
72 -s $sam_output_file 75 -s '$sam_output_file'
76 --biom '$biom_output_file'
73 ]]> 77 ]]>
74 </command> 78 </command>
75 79
76 <inputs> 80 <inputs>
77 <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file" help=""/> 81 <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file" help=""/>
78
79 <conditional name="db"> 82 <conditional name="db">
80 <param name="db_selector" type="select" label="Database with clade-specific marker genes" help=""> 83 <param name="db_selector" type="select" label="Database with clade-specific marker genes" help="">
81 <option value="cached" selected="true">Locally cached</option> 84 <option value="cached" selected="true">Locally cached</option>
82 <option value="history">From history</option> 85 <option value="history">From history</option>
83 </param> 86 </param>
84
85 <when value="cached"> 87 <when value="cached">
86 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" > 88 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" >
87 <options from_data_table="metaphlan2_db" /> 89 <options from_data_table="metaphlan2_database" />
88 </param> 90 </param>
89 </when> 91 </when>
90 <when value="history"> 92 <when value="history">
91 <param name="db_sequences" type="data" format="fasta" label="Database with clade-specific marker genes from history" help="(--bowtie2db)"/> 93 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
92 <param name="db_metadata" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history" help="(--mpa_pkl)"/> 94 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/>
93 </when> 95 </when>
94 </conditional> 96 </conditional>
95
96 <conditional name="analysis_type"> 97 <conditional name="analysis_type">
97 <param name="analysis_type_select" type="select" label="Type of analysis to perform" help="(-t)"> 98 <param name="analysis_type_select" type="select" label="Type of analysis to perform" argument="-t">
98 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option> 99 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
100 <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>
99 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option> 101 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
100 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option> 102 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
101 <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option> 103 <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option>
102 <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option> 104 <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option>
103 <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option> 105 <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
104 </param> 106 </param>
105
106 <when value="rel_ab"> 107 <when value="rel_ab">
107 <param name="taxonomic_level" type="select" label="Taxonomic level for the relative abundance output" help="(--tax_lev)"> 108 <param argument="--taxonomic_level" type="select" label="Taxonomic level for the relative abundance output">
108 <option value="a" selected="true">All taxonomic levels</option> 109 <option value="a" selected="true">All taxonomic levels</option>
109 <option value="k">Kingdoms (Bacteria and Archaea) only</option> 110 <option value="k">Kingdoms (Bacteria and Archaea) only</option>
110 <option value="p">Phyla only</option> 111 <option value="p">Phyla only</option>
111 <option value="c">Classes only</option> 112 <option value="c">Classes only</option>
112 <option value="o">Orders only</option> 113 <option value="o">Orders only</option>
113 <option value="f">Families only</option> 114 <option value="f">Families only</option>
114 <option value="g">Genera only</option> 115 <option value="g">Genera only</option>
115 <option value="s">Species only</option> 116 <option value="s">Species only</option>
116 </param> 117 </param>
117 </when> 118 </when>
118 119 <when value="rel_ab_w_read_stats">
120 <param argument="--taxonomic_level" type="select" label="Taxonomic level for the relative abundance output">
121 <option value="a" selected="true">All taxonomic levels</option>
122 <option value="k">Kingdoms (Bacteria and Archaea) only</option>
123 <option value="p">Phyla only</option>
124 <option value="c">Classes only</option>
125 <option value="o">Orders only</option>
126 <option value="f">Families only</option>
127 <option value="g">Genera only</option>
128 <option value="s">Species only</option>
129 </param>
130 </when>
119 <when value="reads_map"/> 131 <when value="reads_map"/>
120 <when value="clade_profiles"/> 132 <when value="clade_profiles"/>
121
122 <when value="marker_ab_table"> 133 <when value="marker_ab_table">
123 <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"/> 134 <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"/>
124 </when> 135 </when>
125
126 <when value="marker_counts"/> 136 <when value="marker_counts"/>
127
128 <when value="marker_pres_table"> 137 <when value="marker_pres_table">
129 <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/> 138 <param argument="--pres_th" type="integer" value="0" label=" Threshold for calling a marker present"/>
130 </when> 139 </when>
131 </conditional> 140 </conditional>
132 141 <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"/>
133 <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=""/> 142 <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."/>
134 143 <param argument="--ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?"/>
135 <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=""/> 144 <param argument="--ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?"/>
136 145 <param argument="--ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?"/>
137 <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" /> 146 <param argument="--ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?"/>
138 <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" /> 147 <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/>
139 148 <param argument="--sample_id_key" type="text" value="#SampleID" label="Sample ID key"/>
140 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" /> 149 <param argument="--sample_id" type="text" value="Metaphlan2_Analysis" label="Sample ID"/>
141
142 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />
143
144 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
145 </inputs> 150 </inputs>
146 151
147 <outputs> 152 <outputs>
148 <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" /> 153 <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" />
149 <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" /> 154 <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" />
155 <data format="biom" name="biom_output_file" label="${tool.name} on ${on_string}: BIOM file" />
150 </outputs> 156 </outputs>
151 157
152 <tests> 158 <tests>
153 <test> 159 <test>
154 <param name="input_file" value="input_sequences.fasta"/> 160 <param name="input_file" value="input_sequences.fasta"/>
155 <param name="db_selector" value="history" /> 161 <param name="db_selector" value="history" />
156 <param name="db_metadata" value="marker_metadata.json" /> 162 <param name="mpa_pkl" value="marker_metadata.json" />
157 <param name="db_sequences" value="marker_sequences.fasta" /> 163 <param name="bowtie2db" value="marker_sequences.fasta" />
158 <param name="analysis_type_select" value="rel_ab" /> 164 <param name="analysis_type_select" value="rel_ab" />
159 <param name="taxonomic_level" value="a" /> 165 <param name="taxonomic_level" value="a" />
160 <param name="min_cu_len" value="2000" /> 166 <param name="min_cu_len" value="2000" />
161 <param name="min_alignment_len" value="0" /> 167 <param name="min_alignment_len" value="0" />
162 <param name="ignore_viruses" value="" /> 168 <param name="ignore_viruses" value="" />
163 <param name="ignore_eukaryotes" value="" /> 169 <param name="ignore_eukaryotes" value="" />
164 <param name="ignore_bacteria" value="" /> 170 <param name="ignore_bacteria" value="" />
165 <param name="ignore_archaea" value="" /> 171 <param name="ignore_archaea" value="" />
166 <param name="stat_q" value="0.1" /> 172 <param name="stat_q" value="0.1" />
173 <param name="sample_id_key" value="#SampleID"/>
174 <param name="sample_id" value="Metaphlan2_Analysis"/>
167 <output name="output_file" file="community_profile.tabular"/> 175 <output name="output_file" file="community_profile.tabular"/>
168 </test> 176 </test>
169 </tests> 177 </tests>
170 178
171 <help><![CDATA[ 179 <help><![CDATA[
205 213
206 The main output file is a tab-separated file with the predicted taxon relative abundances. 214 The main output file is a tab-separated file with the predicted taxon relative abundances.
207 215
208 ]]></help> 216 ]]></help>
209 217
210 <citations> 218 <expand macro="citations"/>
211 <citation type="doi">10.1038/nmeth.3589</citation>
212 </citations>
213 </tool> 219 </tool>