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comparison metaphlan2.xml @ 25:e8e0f835b4b6 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
author bebatut
date Thu, 31 Mar 2016 03:25:48 -0400
parents 62f9857766e6
children 3f52f2d65d41
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24:51e7d53fcefb 25:e8e0f835b4b6
1 <tool id="metaphlan2" name="MetaPhlAn2" version="0.1.0"> 1 <tool id="metaphlan2" name="MetaPhlAn2" version="2.2.0">
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 <requirements> 5 <requirements>
6 <requirement type="package" version="2.2.4">bowtie2</requirement> 6 <requirement type="package" version="2.2.5">bowtie2</requirement>
7 <requirement type="package" version="2.0">metaphlan2</requirement> 7 <requirement type="package" version="2.2.0">metaphlan2</requirement>
8 </requirements> 8 </requirements>
9 9
10 <stdio> 10 <stdio>
11 <exit_code range="1:" level="fatal" description="" /> 11 <exit_code range="1:" level="fatal" description="" />
12 <regex match="ERROR" 12 <regex match="ERROR"
24 python \${METAPHLAN2_DIR}/metaphlan2.py -v 24 python \${METAPHLAN2_DIR}/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)
31
32 &&
33
30 python \${METAPHLAN2_DIR}/metaphlan2.py 34 python \${METAPHLAN2_DIR}/metaphlan2.py
31 $input_file 35 $input_file
32 -o $output_file 36 -o $output_file
33 37
34 --input_type ${input_file.datatype.file_ext} 38 --input_type ${input_file.datatype.file_ext}
35 --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl 39 --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl
40
41 --bowtie2_exe `which bowtie2`
36 --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200 42 --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200
37 43
38 --no_map 44 --no_map
39 45
40 -t $analysis_type.analysis_type_select 46 -t $analysis_type.analysis_type_select
115 <param name="sam_output" type='boolean' label="Output a sam file?" help="" /> 121 <param name="sam_output" type='boolean' label="Output a sam file?" help="" />
116 <param name="biom_output" type='boolean' label="Output a biom file?" help="" /> 122 <param name="biom_output" type='boolean' label="Output a biom file?" help="" />
117 </inputs> 123 </inputs>
118 124
119 <outputs> 125 <outputs>
120 <data format="txt" name="output_file" 126 <data format="tabular" name="output_file"
121 metadata="input_sequence_file" 127 metadata="input_sequence_file"
122 label="Profile of communities on ${on_string} (MetaPhlAn)" /> 128 label="Profile of communities on ${on_string} (MetaPhlAn)" />
123 129
124 <data format="sam" name="sam_output_file" 130 <data format="sam" name="sam_output_file"
125 metadata="input_sequence_file" 131 metadata="input_sequence_file"
143 <param name="ignore_viruses" value="" /> 149 <param name="ignore_viruses" value="" />
144 <param name="ignore_eukaryotes" value="" /> 150 <param name="ignore_eukaryotes" value="" />
145 <param name="ignore_bacteria" value="" /> 151 <param name="ignore_bacteria" value="" />
146 <param name="ignore_archaea" value="" /> 152 <param name="ignore_archaea" value="" />
147 <param name="stat_q" value="0.1" /> 153 <param name="stat_q" value="0.1" />
148 <param name="sam_output" value='False' /> 154 <param name="sam_output" value='false' />
149 <param name="biom_output" value='True' /> 155 <param name="biom_output" value='true' />
150 <output name="output_file" file="metaphlan2_profiled_metagenome.txt"/> 156 <output name="output_file" file="metaphlan2_profiled_metagenome.txt"/>
151 <output name="biom_output_file" file="metaphlan2_biom.biom"/> 157 <output name="biom_output_file" file="metaphlan2_biom.biom"/>
152 </test> 158 </test>
153 </tests> 159 </tests>
154 160