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comparison metaphlan2.xml @ 20:58e031637111 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 757604ca54eff007917e5f4c4735b1728988c321-dirty
author bebatut
date Fri, 06 Nov 2015 04:04:18 -0500
parents dcd6f25e375b
children 9ab0e6e9d1fb
comparison
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19:dcd6f25e375b 20:58e031637111
33 33
34 --input_type ${input_file.datatype.file_ext} 34 --input_type ${input_file.datatype.file_ext}
35 --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl 35 --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl
36 --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200 36 --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200
37 37
38 #if $bowtie2_output: 38 --no_map
39 --bowtie2out $bowtie2_output_file
40 #else
41 --no_map
42 #end if
43 39
44 -t $analysis_type.analysis_type_select 40 -t $analysis_type.analysis_type_select
45 #if $analysis_type.analysis_type_select == "rel_ab" 41 #if $analysis_type.analysis_type_select == "rel_ab"
46 --tax_lev $analysis_type.taxonomic_level 42 --tax_lev $analysis_type.taxonomic_level
47 #else if $analysis_type.analysis_type_select == "marker_ab_table" 43 #else if $analysis_type.analysis_type_select == "marker_ab_table"
111 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" /> 107 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" />
112 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" /> 108 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />
113 109
114 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/> 110 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
115 111
116 <param name="bowtie2_output" type='boolean' checked="true" label="Store the output of BowTie2?" help="" />
117 <param name="sam_output" type='boolean' label="Output a sam file?" help="" /> 112 <param name="sam_output" type='boolean' label="Output a sam file?" help="" />
118 <param name="biom_output" type='boolean' label="Output a biom file?" help="" /> 113 <param name="biom_output" type='boolean' label="Output a biom file?" help="" />
119 </inputs> 114 </inputs>
120 115
121 <outputs> 116 <outputs>
122 <data format="txt" name="output_file" 117 <data format="txt" name="output_file"
123 metadata="input_sequence_file" 118 metadata="input_sequence_file"
124 label="Profile of communities on ${on_string} (MetaPhlAn)" /> 119 label="Profile of communities on ${on_string} (MetaPhlAn)" />
125
126 <data format="bowtie2" name="bowtie2_output_file"
127 metadata="input_sequence_file"
128 label="Bowtie2 output on ${on_string} (MetaPhlAn)">
129 <filter>bowtie2_output</filter>
130 </data>
131 120
132 <data format="sam" name="sam_output_file" 121 <data format="sam" name="sam_output_file"
133 metadata="input_sequence_file" 122 metadata="input_sequence_file"
134 label="Sam output on ${on_string} (MetaPhlAn)"> 123 label="Sam output on ${on_string} (MetaPhlAn)">
135 <filter>sam_output</filter> 124 <filter>sam_output</filter>
151 <param name="ignore_viruses" value="" /> 140 <param name="ignore_viruses" value="" />
152 <param name="ignore_eukaryotes" value="" /> 141 <param name="ignore_eukaryotes" value="" />
153 <param name="ignore_bacteria" value="" /> 142 <param name="ignore_bacteria" value="" />
154 <param name="ignore_archaea" value="" /> 143 <param name="ignore_archaea" value="" />
155 <param name="stat_q" value="0.1" /> 144 <param name="stat_q" value="0.1" />
156 <param name="bowtie2_output" value='True' />
157 <param name="sam_output" value='False' /> 145 <param name="sam_output" value='False' />
158 <param name="biom_output" value='False' /> 146 <param name="biom_output" value='True' />
159 <output name="output_file" file="profiled_metagenome.txt"/> 147 <output name="output_file" file="profiled_metagenome.txt"/>
148 <output name="biom_output_file" file="biom.biom"/>
160 </test> 149 </test>
161 </tests> 150 </tests>
162 151
163 <help><![CDATA[ 152 <help><![CDATA[
164 153
165 **What it does** 154 **What it does**
166 155
167 MetaPhlAn is a computational tool for profiling the composition of microbial 156 MetaPhlAn is a computational tool for profiling the composition of microbial
168 communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun 157 communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun
169 sequencing data with species level resolution 158 sequencing data with species level resolution. For more information, check the
170 159 `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
171 .. _MetaPhlAn2 user manual: https://bitbucket.org/biobakery/metaphlan2
172 160
173 ----- 161 -----
174 162
175 **Input** 163 **Input**
176 164