Mercurial > repos > iuc > metaphlan2

comparison metaphlan2.xml @ 3:f23f49426a3c draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit bfc25b2695b9689c60101f84162610194a33c886"
author iuc
date Fri, 19 Mar 2021 21:36:43 +0000
parents 5b7ee956d89b
children
comparison
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2:5b7ee956d89b 3:f23f49426a3c
32 #else 32 #else
33 #set ext=$input_file.datatype.file_ext 33 #set ext=$input_file.datatype.file_ext
34 #end if 34 #end if
35 35
36 metaphlan2.py 36 metaphlan2.py
37 '$input_file' 37 #if $input_file.datatype.file_ext.endswith(".gz")
38 <(zcat '$input_file')
39 #else if $input_file.datatype.file_ext.endswith(".bz2")
40 <(bzcat '$input_file')
41 #else
42 '$input_file'
43 #end if
38 -o '$output_file' 44 -o '$output_file'
39 --input_type $ext 45 --input_type $ext
40 --bowtie2_exe `which bowtie2` 46 --bowtie2_exe `which bowtie2`
41 47
42 #if $db.db_selector == "cached" 48 #if $db.db_selector == "cached"
72 -s '$sam_output_file' 78 -s '$sam_output_file'
73 --biom '$biom_output_file' 79 --biom '$biom_output_file'
74 ]]></command> 80 ]]></command>
75 81
76 <inputs> 82 <inputs>
77 <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file"/> 83 <param name="input_file" type="data" format="fastq,fastq.gz,fastq.bz2,fasta,fasta.gz,fasta.bz2,sam" label="Input file"/>
78 <conditional name="db"> 84 <conditional name="db">
79 <param name="db_selector" type="select" label="Database with clade-specific marker genes"> 85 <param name="db_selector" type="select" label="Database with clade-specific marker genes">
80 <option value="cached" selected="true">Locally cached</option> 86 <option value="cached" selected="true">Locally cached</option>
81 <option value="history">From history</option> 87 <option value="history">From history</option>
82 </param> 88 </param>
131 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" /> 137 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />
132 </outputs> 138 </outputs>
133 139
134 <tests> 140 <tests>
135 <test> 141 <test>
136 <param name="input_file" value="input_sequences.fasta"/> 142 <param name="input_file" value="input_sequences.fasta" ftype="fasta"/>
137 <param name="db_selector" value="history" /> 143 <param name="db_selector" value="history" />
138 <param name="mpa_pkl" value="marker_metadata.json" /> 144 <param name="mpa_pkl" value="marker_metadata.json" />
139 <param name="bowtie2db" value="marker_sequences.fasta" /> 145 <param name="bowtie2db" value="marker_sequences.fasta" ftype="fasta"/>
140 <param name="analysis_type_select" value="rel_ab" /> 146 <param name="analysis_type_select" value="rel_ab" />
141 <param name="taxonomic_level" value="a" /> 147 <param name="taxonomic_level" value="a" />
142 <param name="min_cu_len" value="2000" /> 148 <param name="min_cu_len" value="2000" />
143 <param name="min_alignment_len" value="0" /> 149 <param name="min_alignment_len" value="0" />
144 <param name="ignore_viruses" value="" /> 150 <param name="ignore_viruses" value="" />
145 <param name="ignore_eukaryotes" value="" /> 151 <param name="ignore_eukaryotes" value="" />
146 <param name="ignore_bacteria" value="" /> 152 <param name="ignore_bacteria" value="" />
147 <param name="ignore_archaea" value="" /> 153 <param name="ignore_archaea" value="" />
148 <param name="stat_q" value="0.1" /> 154 <param name="stat_q" value="0.1" />
149 <output name="output_file" file="community_profile.tabular"/> 155 <output name="output_file" file="community_profile.tabular" ftype="tabular"/>
156 </test>
157 <test>
158 <param name="input_file" value="input_sequences.fastq.gz" ftype="fastqsanger.gz"/>
159 <param name="db_selector" value="history" />
160 <param name="mpa_pkl" value="marker_metadata.json" />
161 <param name="bowtie2db" value="marker_sequences.fasta" ftype="fasta"/>
162 <param name="analysis_type_select" value="rel_ab" />
163 <param name="taxonomic_level" value="a" />
164 <param name="min_cu_len" value="2000" />
165 <param name="min_alignment_len" value="0" />
166 <param name="ignore_viruses" value="" />
167 <param name="ignore_eukaryotes" value="" />
168 <param name="ignore_bacteria" value="" />
169 <param name="ignore_archaea" value="" />
170 <param name="stat_q" value="0.1" />
171 <output name="output_file" file="community_profile.tabular" ftype="tabular"/>
150 </test> 172 </test>
151 </tests> 173 </tests>
152 174
153 <help><![CDATA[ 175 <help><![CDATA[
154 **What it does** 176 **What it does**