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comparison metaphlan2.xml @ 26:3f52f2d65d41 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty
author bebatut
date Thu, 31 Mar 2016 05:45:29 -0400
parents e8e0f835b4b6
children fb2dc25a832d
comparison
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25:e8e0f835b4b6 26:3f52f2d65d41
76 <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/> 76 <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/>
77 77
78 <conditional name="analysis_type"> 78 <conditional name="analysis_type">
79 <param name="analysis_type_select" type="select" label="Type of analysis to perform"> 79 <param name="analysis_type_select" type="select" label="Type of analysis to perform">
80 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option> 80 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
81 <option value="rel_ab_w_read_stats">Profiling a metagenomes in terms of relative abundances and estimate the number of reads comming from each clade</option>
82 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option> 81 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
83 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option> 82 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
84 <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option> 83 <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option>
84 <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option>
85 <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option> 85 <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
86 </param> 86 </param>
87 <when value="rel_ab"> 87 <when value="rel_ab">
88 <param name="taxonomic_level" type="select" label="Taxonomic level for the relative abundance output"> 88 <param name="taxonomic_level" type="select" label="Taxonomic level for the relative abundance output">
89 <option value="a" selected="true">All taxonomic levels</option> 89 <option value="a" selected="true">All taxonomic levels</option>
94 <option value="f">Families only</option> 94 <option value="f">Families only</option>
95 <option value="g">Genera only</option> 95 <option value="g">Genera only</option>
96 <option value="s">Species only</option> 96 <option value="s">Species only</option>
97 </param> 97 </param>
98 </when> 98 </when>
99 <when value="rel_ab_w_read_stats"/>
100 <when value="reads_map"/> 99 <when value="reads_map"/>
101 <when value="clade_profiles"/> 100 <when value="clade_profiles"/>
102 <when value="marker_ab_table"> 101 <when value="marker_ab_table">
103 <param name="nreads" type="integer" value="0" label="Total number of reads in the original metagenome" help="It is used for normalizing the length-normalized counts with the metagenome size as well. No normalization applied if the value is not specified"/> 102 <param name="nreads" type="integer" value="0" label="Total number of reads in the original metagenome" help="It is used for normalizing the length-normalized counts with the metagenome size as well. No normalization applied if the value is not specified"/>
104 </when> 103 </when>
104 <when value="marker_counts"/>
105 <when value="marker_pres_table"> 105 <when value="marker_pres_table">
106 <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/> 106 <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/>
107 </when> 107 </when>
108 </conditional> 108 </conditional>
109 109