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comparison metaphlan2.xml @ 39:99066fa0645b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'3deaa3adf381c1f3f6134ef6a36074d443f7e3fc\n'-dirty
author bebatut
date Tue, 28 Feb 2017 09:54:26 -0500
parents 4d1bf99ad5ef
children 0cfe385629da
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38:4d1bf99ad5ef 39:99066fa0645b
18 ]]> 18 ]]>
19 </version_command> 19 </version_command>
20 20
21 <command> 21 <command>
22 <![CDATA[ 22 <![CDATA[
23 (which bowtie2 || exit 200)
24
25 &&
26
27 #if $db.db_selector == "history" 23 #if $db.db_selector == "history"
28 mkdir ref_db 24 mkdir ref_db
29 && 25 &&
30 bowtie2-build '$db.bowtie2db' 'ref_db/ref_db' 26 bowtie2-build '$db.bowtie2db' 'ref_db/ref_db'
31 && 27 &&
141 <param argument="--ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?"/> 137 <param argument="--ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?"/>
142 <param argument="--ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?"/> 138 <param argument="--ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?"/>
143 <param argument="--ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?"/> 139 <param argument="--ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?"/>
144 <param argument="--ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?"/> 140 <param argument="--ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?"/>
145 <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/> 141 <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/>
146 <param argument="--sample_id_key" type="text" value="#SampleID" label="Sample ID key"/>
147 <param argument="--sample_id" type="text" value="Metaphlan2_Analysis" label="Sample ID"/>
148 </inputs> 142 </inputs>
149 143
150 <outputs> 144 <outputs>
151 <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" /> 145 <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" />
152 <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" /> 146 <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" />
166 <param name="ignore_viruses" value="" /> 160 <param name="ignore_viruses" value="" />
167 <param name="ignore_eukaryotes" value="" /> 161 <param name="ignore_eukaryotes" value="" />
168 <param name="ignore_bacteria" value="" /> 162 <param name="ignore_bacteria" value="" />
169 <param name="ignore_archaea" value="" /> 163 <param name="ignore_archaea" value="" />
170 <param name="stat_q" value="0.1" /> 164 <param name="stat_q" value="0.1" />
171 <param name="sample_id_key" value="#SampleID"/>
172 <param name="sample_id" value="Metaphlan2_Analysis"/>
173 <output name="output_file" file="community_profile.tabular"/> 165 <output name="output_file" file="community_profile.tabular"/>
174 </test> 166 </test>
175 </tests> 167 </tests>
176 168
177 <help><![CDATA[ 169 <help><![CDATA[