Mercurial > repos > bebatut > metaphlan2

comparison metaphlan2.xml @ 9:31dd7ace2be4 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 90c51a29d5aaab3f8dea67ac12098dc386e23b4e-dirty
author bebatut
date Thu, 05 Nov 2015 08:44:11 -0500
parents 2d1a20517280
children ebe6b7fab320
comparison
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8:2d1a20517280 9:31dd7ace2be4
103 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" /> 103 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" />
104 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" /> 104 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />
105 105
106 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/> 106 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
107 107
108 <param name="bowtie2_output" type='boolean' checked="true" truevalue='' falsevalue='--no_map' label="Store the output of BowTie2?" help="" /> 108 <param name="bowtie2_output" type='boolean' checked="true" truevalue="" falsevalue='--no_map' label="Store the output of BowTie2?" help="" />
109 <param name="sam_output" type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Output a sam file?" help="" /> 109 <param name="sam_output" type='boolean' label="Output a sam file?" help="" />
110 <param name="biom_output" type='boolean' checked="true" truevalue='yes' falsevalue='no' label="Output a biom file?" help="" /> 110 <param name="biom_output" type='boolean' label="Output a biom file?" help="" />
111 </inputs> 111 </inputs>
112 112
113 <outputs> 113 <outputs>
114 <data format_source="txt" name="output_file" 114 <data format="txt" name="output_file"
115 metadata="input_sequence_file" 115 metadata="input_sequence_file"
116 label="Profile of communities on ${on_string} (MetaPhlAn)" /> 116 label="Profile of communities on ${on_string} (MetaPhlAn)" />
117 117
118 <data format_source="bowtie2" name="bowtie2_output_file" 118 <data format="bowtie2" name="bowtie2_output_file"
119 metadata="input_sequence_file" 119 metadata="input_sequence_file"
120 label="Bowtie2 output on ${on_string} (MetaPhlAn)"> 120 label="Bowtie2 output on ${on_string} (MetaPhlAn)">
121 <filter>!bowtie2_output</filter> 121 <filter>bowtie2_output != '--no_map' </filter>
122 </data> 122 </data>
123 123
124 <data format_source="sam" name="sam_output_file" 124 <data format="sam" name="sam_output_file"
125 metadata="input_sequence_file" 125 metadata="input_sequence_file"
126 label="Sam output on ${on_string} (MetaPhlAn)"> 126 label="Sam output on ${on_string} (MetaPhlAn)">
127 <filter>sam_output</filter> 127 <filter>sam_output</filter>
128 </data> 128 </data>
129 <data format_source="biom" name="biom_output_file" 129 <data format="biom" name="biom_output_file"
130 metadata="input_sequence_file" 130 metadata="input_sequence_file"
131 label="Biom output on ${on_string} (MetaPhlAn)"> 131 label="Biom output on ${on_string} (MetaPhlAn)">
132 <filter>biom_output</filter> 132 <filter>biom_output</filter>
133 </data> 133 </data>
134 </outputs> 134 </outputs>
135 135
136 <tests> 136 <tests>
137 <test> 137 <test>
138 <param name="input_file" value="input_sequences.fastq"/> 138 <param name="input_file" value="input_sequences.fastq"/>
139 <param name="analysis_type_select" value="rel_ab" />
140 <param name="taxonomic_level" value="a" />
141 <param name="min_cu_len" value="2000" />
142 <param name="min_alignment_len" value="0" />
143 <param name="ignore_viruses" value="" />
144 <param name="ignore_eukaryotes" value="" />
145 <param name="ignore_bacteria" value="" />
146 <param name="ignore_archaea" value="" />
147 <param name="stat_q" value="0.1" />
148 <param name="bowtie2_output" value='--no_map' />
149 <param name="sam_output" value='False' />
150 <param name="biom_output" value='False' />
139 <output name="output_file" file="profiled_metagenome.txt"/> 151 <output name="output_file" file="profiled_metagenome.txt"/>
140 </test> 152 </test>
141 </tests> 153 </tests>
142 154
143 <help><![CDATA[ 155 <help><![CDATA[