| Previous changeset 0:8c82c4d90cc6 (2017-03-04) Next changeset 2:f60773e921fa (2021-03-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e" |
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modified:
metaphlan2.xml repository_dependencies.xml |
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| diff -r 8c82c4d90cc6 -r 9be4beda6482 metaphlan2.xml --- a/metaphlan2.xml Sat Mar 04 12:23:45 2017 -0500 +++ b/metaphlan2.xml Fri Mar 19 09:38:42 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.0"> +<tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.1"> <description>to profile the composition of microbial communities</description> @@ -10,68 +10,68 @@ <requirement type="package" version="2.3.0">bowtie2</requirement> <requirement type="package" version="2.7.10">python</requirement> </expand> - + <expand macro="stdio"/> - <version_command> -<![CDATA[ -metaphlan2.py -v -]]> - </version_command> + <version_command>metaphlan2.py -v</version_command> - <command> -<![CDATA[ - #if $db.db_selector == "history" - mkdir ref_db - && - bowtie2-build '$db.bowtie2db' 'ref_db/ref_db' - && - python '$__tool_directory__/transform_json_to_pkl.py' - --json_input '$db.mpa_pkl' - --pkl_output 'ref_db/metadata.pkl' - && - #end if + <command><![CDATA[ +#if $db.db_selector == "history" + mkdir ref_db + && + bowtie2-build '$db.bowtie2db' 'ref_db/ref_db' + && + python '$__tool_directory__/transform_json_to_pkl.py' + --json_input '$db.mpa_pkl' + --pkl_output 'ref_db/metadata.pkl' + && +#end if - metaphlan2.py - '$input_file' - -o '$output_file' - --input_type '${input_file.datatype.file_ext}' - --bowtie2_exe `which bowtie2` +#if $input_file.datatype.file_ext.startswith("fastq") + #set ext='fastq' +#else + #set ext=$input_file.datatype.file_ext +#end if + +metaphlan2.py + '$input_file' + -o '$output_file' + --input_type $ext + --bowtie2_exe `which bowtie2` - #if $db.db_selector == "cached" - #set $path = $db.cached_db.fields.path - #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' - #end if + #if $db.db_selector == "cached" + #set $path = $db.cached_db.fields.path + #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' + #end if - --no_map + --no_map - -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.tax_lev' - #else if $analysis_type.analysis_type_select == "marker_ab_table" - --nreads '$analysis_type.nreads' - #else if $analysis_type.analysis_type_select == "marker_pres_table" - --pres_th '$analysis_type.pres_th' - #end if + -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.tax_lev' + #else if $analysis_type.analysis_type_select == "marker_ab_table" + --nreads '$analysis_type.nreads' + #else if $analysis_type.analysis_type_select == "marker_pres_table" + --pres_th '$analysis_type.pres_th' + #end if - --min_cu_len '$min_cu_len' - --min_alignment_len '$min_alignment_len' + --min_cu_len '$min_cu_len' + --min_alignment_len '$min_alignment_len' - $ignore_viruses - $ignore_eukaryotes - $ignore_bacteria - $ignore_archaea + $ignore_viruses + $ignore_eukaryotes + $ignore_bacteria + $ignore_archaea - --stat_q '$stat_q' - -s '$sam_output_file' - --biom '$biom_output_file' -]]> - </command> + --stat_q '$stat_q' + -s '$sam_output_file' + --biom '$biom_output_file' + ]]></command> <inputs> <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file"/> @@ -126,9 +126,9 @@ </inputs> <outputs> - <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" /> - <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" /> - <data format="biom" name="biom_output_file" label="${tool.name} on ${on_string}: BIOM file" /> + <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Community profile" /> + <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file" /> + <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" /> </outputs> <tests> |
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| diff -r 8c82c4d90cc6 -r 9be4beda6482 repository_dependencies.xml --- a/repository_dependencies.xml Sat Mar 04 12:23:45 2017 -0500 +++ b/repository_dependencies.xml Fri Mar 19 09:38:42 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <repositories description="This requires the MetaPhlAn2 data manager definition to install all required databases."> - <repository changeset_revision="9c4ad82be5bd" name="data_manager_metaphlan2_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories> + <repository name="data_manager_metaphlan2_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="83f07f40b200"/> +</repositories> \ No newline at end of file |