Mercurial > repos > bebatut > metaphlan2
comparison metaphlan2.xml @ 44:34114d4670fe draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit b'cf8373aeed58964f1d139a23cd1ec4698683c60e\n'-dirty
| author | bebatut |
|---|---|
| date | Thu, 02 Mar 2017 11:28:35 -0500 |
| parents | 5af453f55e31 |
| children |
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| 43:1767fd901e8c | 44:34114d4670fe |
|---|---|
| 38 --input_type '${input_file.datatype.file_ext}' | 38 --input_type '${input_file.datatype.file_ext}' |
| 39 --bowtie2_exe `which bowtie2` | 39 --bowtie2_exe `which bowtie2` |
| 40 | 40 |
| 41 #if $db.db_selector == "cached" | 41 #if $db.db_selector == "cached" |
| 42 #set $path = $db.cached_db.fields.path | 42 #set $path = $db.cached_db.fields.path |
| 43 --bowtie2db `ls $path/*.pkl | sed 's/\(.*\)\..*/\1/'` | 43 #set $value = $db.cached_db.fields.value |
| 44 --mpa_pkl `ls $path/*.pkl` | 44 --bowtie2db $path/$value |
| 45 --mpa_pkl $path/$value'.pkl' | |
| 45 #else | 46 #else |
| 46 --bowtie2db 'ref_db/ref_db' | 47 --bowtie2db 'ref_db/ref_db' |
| 47 --mpa_pkl 'ref_db/metadata.pkl' | 48 --mpa_pkl 'ref_db/metadata.pkl' |
| 48 #end if | 49 #end if |
| 49 | 50 |
| 50 --no_map | 51 --no_map |
| 51 | 52 |
| 52 -t '$analysis_type.analysis_type_select' | 53 -t '$analysis_type.analysis_type_select' |
| 53 #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats" | 54 #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats" |
| 54 --tax_lev '$analysis_type.taxonomic_level' | 55 --tax_lev '$analysis_type.tax_lev' |
| 55 #else if $analysis_type.analysis_type_select == "marker_ab_table" | 56 #else if $analysis_type.analysis_type_select == "marker_ab_table" |
| 56 --nreads '$analysis_type.nreads' | 57 --nreads '$analysis_type.nreads' |
| 57 #else if $analysis_type.analysis_type_select == "marker_pres_table" | 58 #else if $analysis_type.analysis_type_select == "marker_pres_table" |
| 58 --pres_th '$analysis_type.pres_th' | 59 --pres_th '$analysis_type.pres_th' |
| 59 #end if | 60 #end if |
| 89 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/> | 90 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/> |
| 90 </when> | 91 </when> |
| 91 </conditional> | 92 </conditional> |
| 92 <conditional name="analysis_type"> | 93 <conditional name="analysis_type"> |
| 93 <param name="analysis_type_select" type="select" label="Type of analysis to perform" argument="-t"> | 94 <param name="analysis_type_select" type="select" label="Type of analysis to perform" argument="-t"> |
| 94 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option> | 95 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option> |
| 95 <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> | 96 <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> |
| 96 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option> | 97 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option> |
| 97 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option> | 98 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option> |
| 98 <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option> | 99 <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option> |
| 99 <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option> | 100 <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option> |
| 100 <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option> | 101 <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option> |
| 101 </param> | 102 </param> |
| 102 <when value="rel_ab"> | 103 <when value="rel_ab"> |
| 103 <param argument="--taxonomic_level" type="select" label="Taxonomic level for the relative abundance output"> | 104 <expand macro="tax_lev"/> |
| 104 <option value="a" selected="true">All taxonomic levels</option> | |
| 105 <option value="k">Kingdoms (Bacteria and Archaea) only</option> | |
| 106 <option value="p">Phyla only</option> | |
| 107 <option value="c">Classes only</option> | |
| 108 <option value="o">Orders only</option> | |
| 109 <option value="f">Families only</option> | |
| 110 <option value="g">Genera only</option> | |
| 111 <option value="s">Species only</option> | |
| 112 </param> | |
| 113 </when> | 105 </when> |
| 114 <when value="rel_ab_w_read_stats"> | 106 <when value="rel_ab_w_read_stats"> |
| 115 <param argument="--taxonomic_level" type="select" label="Taxonomic level for the relative abundance output"> | 107 <expand macro="tax_lev"/> |
| 116 <option value="a" selected="true">All taxonomic levels</option> | |
| 117 <option value="k">Kingdoms (Bacteria and Archaea) only</option> | |
| 118 <option value="p">Phyla only</option> | |
| 119 <option value="c">Classes only</option> | |
| 120 <option value="o">Orders only</option> | |
| 121 <option value="f">Families only</option> | |
| 122 <option value="g">Genera only</option> | |
| 123 <option value="s">Species only</option> | |
| 124 </param> | |
| 125 </when> | 108 </when> |
| 126 <when value="reads_map"/> | 109 <when value="reads_map"/> |
| 127 <when value="clade_profiles"/> | 110 <when value="clade_profiles"/> |
| 128 <when value="marker_ab_table"> | 111 <when value="marker_ab_table"> |
| 129 <param argument="--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"/> | 112 <param argument="--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"/> |