Mercurial > repos > iuc > cami_amber
changeset 1:afc795d10918 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/ commit eec9d5fede4b4b81bd163e00a1654bd33c589fb3
| author | iuc |
|---|---|
| date | Tue, 04 Jun 2024 11:41:41 +0000 |
| parents | 6c71acde9d52 |
| children | f801b844f239 |
| files | cami_amber_add_length.xml cami_amber_convert_to_biobox.xml |
| diffstat | 2 files changed, 0 insertions(+), 252 deletions(-) [+] |
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--- a/cami_amber_add_length.xml Mon May 20 18:08:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,90 +0,0 @@ -<tool id="cami_amber_add" name="CAMI AMBER add length column" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> - <description>Create gold standard file for CAMI AMBER</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"> - <![CDATA[ - - ln -s '${gold_standard_file}' '$gold_standard_file.element_identifier' && - ln -s '${fasta_file}' '$fasta_file.element_identifier' && - - add_length_column.py - -g '$gold_standard_file.element_identifier' - -f '$fasta_file.element_identifier' - > gold_standard_file.tsv - ]]> - </command> - <inputs> - <param argument="--gold_standard_file" type="data" format="tabular" - label="Input gold standard file here" - help="Input a binning file in biobox format to generate a biobox format file with the extra column 'Length' which is needed for AMBER. Every other biobox format can be used for this as well!" /> - <param argument="--fasta_file" type="data" format="fasta,fasta.gz,fastq,fastq.gz" - label="Input fasta/fastq file here" - help="Input the file which match to the gold standard file" /> - </inputs> - <outputs> - <data name="file" format="tabular" from_work_dir="gold_standard_file.tsv" label="${tool.name}: Gold standard file" /> - </outputs> - <tests> - <test expect_num_outputs="1"> - <param name="gold_standard_file" value="test_add.tsv" ftype="tabular" /> - <param name="fasta_file" value="test_add.fasta.gz" ftype="fasta.gz" /> - <output name="file" > - <assert_contents> - <has_size value="124000" delta="3000" /> - </assert_contents> - </output> - </test> - </tests> - <help> - <![CDATA[ - .. class:: infomark - - **What it does** - - This tool can create the gold standard file which has to be used for the CAMI AMBER. - - **Input** - - This tool required 2 inputs: - - - A binning file (biobox format) - - This file can be created via the convert_to_biobox tool - - .. class:: infomark - - Example(tab separated): - - :: - - #CAMI Format for Binning - @Version:0.9.0 - @SampleID:CAMI_low - @@SEQUENCEID BINID - RL|S1|C10 Bin_034 - RL|S1|C100 Bin_023 - RL|S1|C1000 Bin_034 - RL|S1|C10000 Bin_019 - RL|S1|C10002 Bin_035 - RL|S1|C10004 Bin_035 - RL|S1|C10008 Bin_034 - RL|S1|C10011 Bin_035 - RL|S1|C10012 Bin_013 - RL|S1|C10014 Bin_035 - - - A fasta/fastq file (fasta,fasta.gz,fastq,fastq.gz format) - - This file need the identical sequences which are in the gold standard file to create the finish gold standard file for CAMI AMBER - - **Output** - - As output the tool give you out a file in biobox format with the added column 'Length'. This file then can be used for AMBER as example! - - - ]]> - </help> - <expand macro="citations" /> -</tool>
--- a/cami_amber_convert_to_biobox.xml Mon May 20 18:08:36 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,162 +0,0 @@ -<tool id="cami_amber_convert" name="CAMI AMBER convert to biobox" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> - <description>Create binning file(s) for CAMI AMBER</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"> - <![CDATA[ - - mkdir -p output - - #for $file in $input.files: - && - ln -s '$file' './$file.element_identifier' - #end for - - #if $work == "single": - #for $file in $input.files: - && - #set $out = $file.element_identifier.split('.')[0] + '.tsv' - convert_fasta_bins_to_biobox_format.py - -o 'output/$out' - '$file.element_identifier' - #end for - #else: - && - convert_fasta_bins_to_biobox_format.py - -o 'output/binning.tsv' - #for $file in $input.files: - '$file.element_identifier' - #end for - #end if - - ]]> - </command> - <inputs> - <param name="work" type="select" label="Merge binning output files?" - help="If yes all input files will be merged into one biobox output (required input by amber). If no each input will be converted into a separate biobox output file." > - <option value="single">Each file alone</option> - <option value="all">All together</option> - </param> - <conditional name="input"> - <param name="is_select" type="select" label="Choose how to input the files" - help="You can provide each input separately or as a collection"> - <option value="manually">Manually</option> - <option value="data">Data collection</option> - </param> - <when value="manually"> - <param name="files" type="data" format="fasta" multiple="true" - label="Input fasta files" - help="Input all fasta files which this tool should convert into biobox format" /> - </when> - <when value="data"> - <param name="files" type="data_collection" collection_type="list" format="fasta" - label="Input the fasta collection" - help="Input the fasta collected which the tool should convert into biobox format" /> - </when> - </conditional> - </inputs> - <outputs> - <data name="binning_file" format="tabular" from_work_dir="output/binning.tsv" label="${tool.name}: BINNING FILE"> - <filter>work and "all" in work</filter> - </data> - <collection name="binning_collection" type="list" label="${tool.name}: BINNING COLLECTION" > - <discover_datasets pattern="(?P<designation>.+)\.tsv" format="tabular" directory="output/" recurse="true" /> - <filter>work and "single" in work</filter> - </collection> - </outputs> - <tests> - <test expect_num_outputs="1" > - <param name="work" value="single" /> - <conditional name="input" > - <param name="is_select" value="manually" /> - <param name="files" value="test_add1.fasta,test_add2.fasta" ftype="fasta" /> - </conditional> - <output_collection name="binning_collection" type="list"> - <element name="test_add1" > - <assert_contents> - <has_n_lines n="1464" /> - </assert_contents> - </element> - <element name="test_add2" > - <assert_contents> - <has_n_lines n="36" /> - </assert_contents> - </element> - </output_collection> - </test> - <test expect_num_outputs="1" > - <param name="work" value="single" /> - <conditional name="input" > - <param name="is_select" value="data" /> - <param name="files" > - <collection name="test" type="list" > - <element name="test_add1" value="test_add1.fasta" /> - <element name="test_add2" value="test_add2.fasta" /> - </collection> - </param> - </conditional> - <output_collection name="binning_collection" type="list"> - <element name="test_add1" > - <assert_contents> - <has_n_lines n="1464" /> - </assert_contents> - </element> - <element name="test_add2" > - <assert_contents> - <has_n_lines n="36" /> - </assert_contents> - </element> - </output_collection> - </test> - <test expect_num_outputs="1" > - <param name="work" value="all" /> - <conditional name="input" > - <param name="is_select" value="manually" /> - <param name="files" value="test_add1.fasta,test_add2.fasta" ftype="fasta" /> - </conditional> - <output name="binning_file"> - <assert_contents> - <has_n_lines n="1496" /> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1" > - <param name="work" value="all" /> - <conditional name="input" > - <param name="is_select" value="data" /> - <param name="files" > - <collection name="test" type="list" > - <element name="test_add1" value="test_add1.fasta" /> - <element name="test_add2" value="test_add2.fasta" /> - </collection> - </param> - </conditional> - <output name="binning_file"> - <assert_contents> - <has_n_lines n="1496" /> - </assert_contents> - </output> - </test> - </tests> - <help> - <![CDATA[ - .. class:: infomark - - **What it does** - - This tool can create a tsv file in biobox format or a collection of multiple files. - - **Input** - - This tool required only fasta files. You can submit n files manually or a collection of fasta files. - - **Output** - - This tool either give out 1 binning file in biobox format or for each inputted file 1 binning file in biobox format. - - ]]> - </help> - <expand macro="citations" /> -</tool>