Mercurial > repos > bebatut > metaphlan2
comparison metaphlan2.xml @ 27:fb2dc25a832d draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
author | bebatut |
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date | Tue, 12 Apr 2016 03:07:32 -0400 |
parents | 3f52f2d65d41 |
children | 1d993cca38e3 |
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26:3f52f2d65d41 | 27:fb2dc25a832d |
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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 |