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comparison metaphlan.xml @ 11:75c7ed7d4ff2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit e567b31e44ef8525e6667b37480b6f1b599224b9
author iuc
date Fri, 21 Feb 2025 21:28:59 +0000
parents 392430381492
children 2e850e8ebc71
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10:392430381492 11:75c7ed7d4ff2
1 <tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@"> 1 <tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
2 <description>to profile the composition of microbial communities</description> 2 <description>to profile the composition of microbial communities</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="tax_lev"> 5 <xml name="tax_lev">
6 <conditional name="tax_lev"> 6 <conditional name="tax_lev">
181 --ignore_bacteria 181 --ignore_bacteria
182 #end if 182 #end if
183 #if 'ignore_archaea' in $analysis.organism_profiling 183 #if 'ignore_archaea' in $analysis.organism_profiling
184 --ignore_archaea 184 --ignore_archaea
185 #end if 185 #end if
186 --stat $analysis.stat
186 --stat_q $analysis.stat_q 187 --stat_q $analysis.stat_q
187 --perc_nonzero $analysis.perc_nonzero 188 --perc_nonzero $analysis.perc_nonzero
188 #if $analysis.ignore_markers 189 #if $analysis.ignore_markers
189 --ignore_markers '$analysis.ignore_markers' 190 --ignore_markers '$analysis.ignore_markers'
190 #end if 191 #end if
1137 <conditional name="db"> 1138 <conditional name="db">
1138 <param name="db_selector" value="cached"/> 1139 <param name="db_selector" value="cached"/>
1139 <param name="cached_db" value="test-db-20210409"/> 1140 <param name="cached_db" value="test-db-20210409"/>
1140 </conditional> 1141 </conditional>
1141 </section> 1142 </section>
1142 <conditional name="in">
1143 <param name="selector" value="bowtie2out"/>
1144 <param name="in" value="SRS014464-Anterior_nares-bowtie2out.tabular"/>
1145 </conditional>
1146 <section name="mapping">
1147 <param name="bt2_ps" value="sensite"/>
1148 <param name="min_mapq_val" value="5"/>
1149 </section>
1150 <section name="analysis"> 1143 <section name="analysis">
1151 <conditional name="analysis_type"> 1144 <conditional name="analysis_type">
1152 <param name="t" value="rel_ab"/> 1145 <param name="t" value="rel_ab"/>
1153 <conditional name="tax_lev"> 1146 <conditional name="tax_lev">
1154 <param name="tax_lev" value="a"/> 1147 <param name="tax_lev" value="a"/>
1352 <param name="t" value="marker_ab_table"/> 1345 <param name="t" value="marker_ab_table"/>
1353 </conditional> 1346 </conditional>
1354 </section> 1347 </section>
1355 <conditional name="viral_analysis"> 1348 <conditional name="viral_analysis">
1356 <param name="profile_vsc" value="--profile_vsc"/> 1349 <param name="profile_vsc" value="--profile_vsc"/>
1357 <param name="vsc_out" value="true"/>
1358 </conditional> 1350 </conditional>
1359 <conditional name="subsample"> 1351 <conditional name="subsample">
1360 <param name="selector" value="single"/> 1352 <param name="selector" value="single"/>
1361 <param name="subsampling" value="10000"/> 1353 <param name="subsampling" value="10000"/>
1362 <param name="subsampling_seed" value="42"/> 1354 <param name="subsampling_seed" value="42"/>