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comparison metaphlan2.xml @ 17:bee6cb51b96d draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit bf4b8a62e4414d68a917f5b72f3aedf34facaff2-dirty
author bebatut
date Thu, 05 Nov 2015 10:31:59 -0500
parents 84dd21255542
children 1aaa528861e6
comparison
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16:84dd21255542 17:bee6cb51b96d
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 $bowtie2_output 38 # if $bowtie2_output:
39 #if not $bowtie2_output
40 --bowtie2out $bowtie2_output_file 39 --bowtie2out $bowtie2_output_file
40 # else:
41 --no_map
41 #end if 42 #end if
42 43
43 -t $analysis_type.analysis_type_select 44 -t $analysis_type.analysis_type_select
44 #if $analysis_type.analysis_type_select == "rel_ab" 45 #if $analysis_type.analysis_type_select == "rel_ab"
45 --tax_lev $analysis_type.taxonomic_level 46 --tax_lev $analysis_type.taxonomic_level
110 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" /> 111 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" />
111 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" /> 112 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />
112 113
113 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/> 114 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
114 115
115 <param name="bowtie2_output" type='boolean' checked="true" truevalue="" falsevalue='--no_map' label="Store the output of BowTie2?" help="" /> 116 <param name="bowtie2_output" type='boolean' checked="true" label="Store the output of BowTie2?" help="" />
116 <param name="sam_output" type='boolean' label="Output a sam file?" help="" /> 117 <param name="sam_output" type='boolean' label="Output a sam file?" help="" />
117 <param name="biom_output" type='boolean' label="Output a biom file?" help="" /> 118 <param name="biom_output" type='boolean' label="Output a biom file?" help="" />
118 </inputs> 119 </inputs>
119 120
120 <outputs> 121 <outputs>
123 label="Profile of communities on ${on_string} (MetaPhlAn)" /> 124 label="Profile of communities on ${on_string} (MetaPhlAn)" />
124 125
125 <data format="bowtie2" name="bowtie2_output_file" 126 <data format="bowtie2" name="bowtie2_output_file"
126 metadata="input_sequence_file" 127 metadata="input_sequence_file"
127 label="Bowtie2 output on ${on_string} (MetaPhlAn)"> 128 label="Bowtie2 output on ${on_string} (MetaPhlAn)">
128 <filter>bowtie2_output != '--no_map' </filter> 129 <filter>bowtie2_output</filter>
129 </data> 130 </data>
130 131
131 <data format="sam" name="sam_output_file" 132 <data format="sam" name="sam_output_file"
132 metadata="input_sequence_file" 133 metadata="input_sequence_file"
133 label="Sam output on ${on_string} (MetaPhlAn)"> 134 label="Sam output on ${on_string} (MetaPhlAn)">
150 <param name="ignore_viruses" value="" /> 151 <param name="ignore_viruses" value="" />
151 <param name="ignore_eukaryotes" value="" /> 152 <param name="ignore_eukaryotes" value="" />
152 <param name="ignore_bacteria" value="" /> 153 <param name="ignore_bacteria" value="" />
153 <param name="ignore_archaea" value="" /> 154 <param name="ignore_archaea" value="" />
154 <param name="stat_q" value="0.1" /> 155 <param name="stat_q" value="0.1" />
155 <param name="bowtie2_output" value='--no_map' /> 156 <param name="bowtie2_output" value='True' />
156 <param name="sam_output" value='False' /> 157 <param name="sam_output" value='False' />
157 <param name="biom_output" value='False' /> 158 <param name="biom_output" value='False' />
158 <output name="output_file" file="profiled_metagenome.txt"/> 159 <output name="output_file" file="profiled_metagenome.txt"/>
159 </test> 160 </test>
160 </tests> 161 </tests>