comparison metaphlan2.xml @ 27:fb2dc25a832d draft

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
comparison
equal deleted inserted replaced
26:3f52f2d65d41 27:fb2dc25a832d
19 description="" /> 19 description="" />
20 </stdio> 20 </stdio>
21 21
22 <version_command> 22 <version_command>
23 <![CDATA[ 23 <![CDATA[
24 python \${METAPHLAN2_DIR}/metaphlan2.py -v 24 metaphlan2.py -v
25 ]]> 25 ]]>
26 </version_command> 26 </version_command>
27 27
28 <command> 28 <command>
29 <![CDATA[ 29 <![CDATA[
30 (which bowtie2 || exit 200) 30 (which bowtie2 || exit 200)
31 31
32 && 32 &&
33 33
34 python \${METAPHLAN2_DIR}/metaphlan2.py 34 metaphlan2.py
35 $input_file 35 $input_file
36 -o $output_file 36 -o $output_file
37 37
38 --input_type ${input_file.datatype.file_ext} 38 --input_type ${input_file.datatype.file_ext}
39 --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl 39
40 #set $data_table = dict([(_[0], _[2]) for _ in $mpa_pkl.input.options.tool_data_table.data])
41 #set $db = $mpa_pkl.value
42 --mpa_pkl $data_table[$db]
40 43
41 --bowtie2_exe `which bowtie2` 44 --bowtie2_exe `which bowtie2`
42 --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200 45
46 #set $data_table = dict([(_[0], _[2]) for _ in $bowtie2db.input.options.tool_data_table.data])
47 #set $db = $bowtie2db.value
48 --bowtie2db $data_table[$db]
43 49
44 --no_map 50 --no_map
45 51
46 -t $analysis_type.analysis_type_select 52 -t $analysis_type.analysis_type_select
47 #if $analysis_type.analysis_type_select == "rel_ab" 53 #if $analysis_type.analysis_type_select == "rel_ab"
72 ]]> 78 ]]>
73 </command> 79 </command>
74 80
75 <inputs> 81 <inputs>
76 <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/> 82 <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/>
83
84 <param name="mpa_pkl" label="Metadata" type="select" >
85 <options from_data_table="metaphlan2_metadata" />
86 </param>
87
88 <param name="bowtie2db" label="BowTie2 database" type="select" >
89 <options from_data_table="metaphlan2_bowtie_db" />
90 </param>
77 91
78 <conditional name="analysis_type"> 92 <conditional name="analysis_type">
79 <param name="analysis_type_select" type="select" label="Type of analysis to perform"> 93 <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> 94 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
81 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option> 95 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
140 </outputs> 154 </outputs>
141 155
142 <tests> 156 <tests>
143 <test> 157 <test>
144 <param name="input_file" value="metaphlan2_input_sequences.fastq"/> 158 <param name="input_file" value="metaphlan2_input_sequences.fastq"/>
159 <param name="mpa_pkl" value="" />
160 <param name="bowtie2db" value="" />
145 <param name="analysis_type_select" value="rel_ab" /> 161 <param name="analysis_type_select" value="rel_ab" />
146 <param name="taxonomic_level" value="a" /> 162 <param name="taxonomic_level" value="a" />
147 <param name="min_cu_len" value="2000" /> 163 <param name="min_cu_len" value="2000" />
148 <param name="min_alignment_len" value="0" /> 164 <param name="min_alignment_len" value="0" />
149 <param name="ignore_viruses" value="" /> 165 <param name="ignore_viruses" value="" />
150 <param name="ignore_eukaryotes" value="" /> 166 <param name="ignore_eukaryotes" value="" />
151 <param name="ignore_bacteria" value="" /> 167 <param name="ignore_bacteria" value="" />
152 <param name="ignore_archaea" value="" /> 168 <param name="ignore_archaea" value="" />
153 <param name="stat_q" value="0.1" /> 169 <param name="stat_q" value="0.1" />
154 <param name="sam_output" value='false' /> 170 <param name="sam_output" value='false' />
155 <param name="biom_output" value='true' /> 171 <param name="biom_output" value='false' />
156 <output name="output_file" file="metaphlan2_profiled_metagenome.txt"/> 172 <output name="output_file" file="metaphlan2_profiled_metagenome.txt"/>
157 <output name="biom_output_file" file="metaphlan2_biom.biom"/>
158 </test> 173 </test>
159 </tests> 174 </tests>
160 175
161 <help><![CDATA[ 176 <help><![CDATA[
162 177