Mercurial > repos > bebatut > metaphlan2
changeset 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 | 1767fd901e8c |
| children | |
| files | metaphlan2.xml metaphlan2_macros.xml repository_dependencies.xml |
| diffstat | 3 files changed, 26 insertions(+), 31 deletions(-) [+] |
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--- a/metaphlan2.xml Wed Mar 01 11:07:43 2017 -0500 +++ b/metaphlan2.xml Thu Mar 02 11:28:35 2017 -0500 @@ -40,8 +40,9 @@ #if $db.db_selector == "cached" #set $path = $db.cached_db.fields.path - --bowtie2db `ls $path/*.pkl | sed 's/\(.*\)\..*/\1/'` - --mpa_pkl `ls $path/*.pkl` + #set $value = $db.cached_db.fields.value + --bowtie2db $path/$value + --mpa_pkl $path/$value'.pkl' #else --bowtie2db 'ref_db/ref_db' --mpa_pkl 'ref_db/metadata.pkl' @@ -51,7 +52,7 @@ -t '$analysis_type.analysis_type_select' #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats" - --tax_lev '$analysis_type.taxonomic_level' + --tax_lev '$analysis_type.tax_lev' #else if $analysis_type.analysis_type_select == "marker_ab_table" --nreads '$analysis_type.nreads' #else if $analysis_type.analysis_type_select == "marker_pres_table" @@ -91,37 +92,19 @@ </conditional> <conditional name="analysis_type"> <param name="analysis_type_select" type="select" label="Type of analysis to perform" argument="-t"> - <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option> - <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> - <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option> - <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option> - <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option> - <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option> - <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option> + <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option> + <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> + <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option> + <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option> + <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option> + <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option> + <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option> </param> <when value="rel_ab"> - <param argument="--taxonomic_level" type="select" label="Taxonomic level for the relative abundance output"> - <option value="a" selected="true">All taxonomic levels</option> - <option value="k">Kingdoms (Bacteria and Archaea) only</option> - <option value="p">Phyla only</option> - <option value="c">Classes only</option> - <option value="o">Orders only</option> - <option value="f">Families only</option> - <option value="g">Genera only</option> - <option value="s">Species only</option> - </param> + <expand macro="tax_lev"/> </when> <when value="rel_ab_w_read_stats"> - <param argument="--taxonomic_level" type="select" label="Taxonomic level for the relative abundance output"> - <option value="a" selected="true">All taxonomic levels</option> - <option value="k">Kingdoms (Bacteria and Archaea) only</option> - <option value="p">Phyla only</option> - <option value="c">Classes only</option> - <option value="o">Orders only</option> - <option value="f">Families only</option> - <option value="g">Genera only</option> - <option value="s">Species only</option> - </param> + <expand macro="tax_lev"/> </when> <when value="reads_map"/> <when value="clade_profiles"/>
--- a/metaphlan2_macros.xml Wed Mar 01 11:07:43 2017 -0500 +++ b/metaphlan2_macros.xml Thu Mar 02 11:28:35 2017 -0500 @@ -25,4 +25,16 @@ <citation type="doi">10.1038/nmeth.3589</citation> </citations> </xml> + <xml name="tax_lev"> + <param argument="--tax_lev" type="select" label="Taxonomic level for the relative abundance output"> + <option value="a" selected="true">All taxonomic levels</option> + <option value="k">Kingdoms (Bacteria and Archaea) only</option> + <option value="p">Phyla only</option> + <option value="c">Classes only</option> + <option value="o">Orders only</option> + <option value="f">Families only</option> + <option value="g">Genera only</option> + <option value="s">Species only</option> + </param> + </xml> </macros>
--- a/repository_dependencies.xml Wed Mar 01 11:07:43 2017 -0500 +++ b/repository_dependencies.xml Thu Mar 02 11:28:35 2017 -0500 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the MetaPhlAn2 data manager definition to install all required databases."> - <repository changeset_revision="8602983cb86f" name="data_manager_metaphlan2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="bf858d6f7365" name="data_manager_metaphlan2_database_downloader" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>