Mercurial > repos > brenninc > xdirectory_reader_limited_by_data_table
changeset 7:1d1b8eb0e6b7 draft
Deleted selected files
| author | brenninc |
|---|---|
| date | Mon, 09 May 2016 02:06:24 -0400 |
| parents | 971629438ca4 |
| children | 288a172e95aa |
| files | data_reader.xml |
| diffstat | 1 files changed, 0 insertions(+), 428 deletions(-) [+] |
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--- a/data_reader.xml Mon May 09 02:06:20 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,428 +0,0 @@ -<tool id="directory_data_reader" name="Directory Data Finder" version="0.2"> - <description>Reads a particular data type from a directory on the server</description> - <command interpreter="python"> -<![CDATA[ - directory_copier.py - #if $results.required=="data" - --ending .${results.extension.file_type} - --link - #if $results.start - --start $results.start - #end if - #if $results.last - --last $results.last - #end if - #if $results.extension.file_type=="fa" - --new_ending .fasta - #end if - #if $results.extension.file_type=="fq" - --new_ending .fastq - #end if - #if $results.extension.file_type=="text" - --new_ending .txt - #end if - #if $results.extension.file_type=="tsv" - --new_ending .tabular - #end if - #if $results.extension.file_type in ["fasta.gz"] - --decompress - --new_ending .fasta - #end if - #if $results.extension.file_type=="fastq" - --new_ending .$results.extension.new_galaxy.new_ending - #end if - #if $results.extension.file_type=="fastq.gz" - --decompress - --new_ending .${results.extension.new_galaxy.new_ending} - #end if - #else - --ending bam - --ending csv - --ending fa - --ending fasta - --ending fasta.gz - --ending fastq - --ending fastq.gz - --ending fasta - --ending fq - --ending sam - --ending tabular - --ending text - --ending tsv - --ending txt - --ending xls - --ending xlsx - #end if - #if $directory.startswith('/'): - --path ${directory} - #else - --path $__tool_directory__/${directory} - #end if - --list ${listing} -]]> - </command> - <inputs> - <param name="directory" type="text" label="Directory to read data from." /> - <param name="list_name" type="text" size="25" label="output name" value="input data"/> - <conditional name="results"> - <param name="required" type="select" label="Download data or just directory listing" help="Select type of action required."> - <option value="data" selected="true">Data and listing of selected type</option> - <option value="listing">Get listing of selected file types </option> - </param> - <when value="data"> - <param name="start" type="text" value="" label="String which must be at the start of each file name" /> - <param name="last" type="text" value="" label="String which must be at the end of the file name (excluding the file type)" /> - <conditional name="extension"> - <param name="file_type" type="select" label="File Type" help="File Type."> - <option value="bam">*.bam files</option> - <option value="csv">*.csv files</option> - <option value="fa">*.fa files Files saved as *.fasta for galaxy</option> - <option value="fasta">*.fasta files</option> - <option value="fasta.gz">*.fasta.gz files</option> - <option value="fastq">*.fastq files</option> - <option value="fastq.gz">*.fastq.gz files</option> - <option value="fastq">*.fastq files</option> - <option value="fastq.gz">*.fastq.gz files</option> - <option value="fq">*.fq files Files saved as *.fastq for galaxy</option> - <option value="sam">*.sam files</option> - <option value="tabular">*.tabular Files</option> - <option value="text">*.text Files saved as *.txt for galaxy</option> - <option value="tsv">*.tsv files saved as *.tabular for galaxy</option> - <option value="txt">*.txt Files</option> - <option value="xls">*.xls files</option> - <option value="xlsx">*.xlsx files</option> - </param> - <when value="bam" /> - <when value="csv" /> - <when value="fa" /> - <when value="fasta" /> - <when value="fasta.gz" /> - <when value="fastq" > - <conditional name="new_galaxy"> - <param name="new_ending" type="select" label="Ending to be used for Galaxy" help="Will determine which down stream tools can be used."> - <option value="fastq" selected="true">Keep data as general fastq format</option> - <option value="fastqsanger">Tag data as fastq sanger in galaxy</option> - <option value="fastqsolexa">Tag data as fastq solexa in galaxy</option> - <option value="fastqillumina">Tag data as fastq illumina in galaxy</option> - </param> - <when value="fastq" /> - <when value="fastqsanger" /> - <when value="fastqsolexa" /> - <when value="fastqillumina" /> - </conditional> - </when> - <when value="fastq.gz" > - <conditional name="new_galaxy"> - <param name="new_ending" type="select" label="Ending to be used for Galaxy" help="Will determine which down stream tools can be used."> - <option value="fastq" selected="true" >Keep data as general fastq format</option> - <option value="fastqsanger">Tag data as fastq sanger in galaxy</option> - <option value="fastqsolexa">Tag data as fastq solexa in galaxy</option> - <option value="fastqillumina">Tag data as fastq illumina in galaxy</option> - </param> - <when value="fastq" /> - <when value="fastqsanger" /> - <when value="fastqsolexa" /> - <when value="fastqillumina" /> - </conditional> - </when> - <when value="fq" /> - <when value="sam" /> - <when value="tabular" /> - <when value="text" /> - <when value="tsv" /> - <when value="txt" /> - <when value="xls" /> - <when value="xlsx" /> - </conditional> - </when> - <when value="listing"> - </when> - </conditional> - </inputs> - <outputs> - <data format="txt" name="listing" label="List of files in $list_name"> - </data> - <!-- Ideally galaxy can get the type based on the file extensions. If so just add the type here --> - <collection type="list" label="$list_name" name="data_collection"> - <filter>(results['required'] == 'data')</filter> - <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true" /> - </collection> - </outputs> - <tests> - <test> - <param name="directory" value="test-data" /> - <param name="list_name" value="csv_files" /> - <param name="results|extension|file_type" value="csv"/> - <output name="listing"> - <assert_contents> - <has_line line="sample1.csv" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="csv" file="sample1.csv" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="fa"/> - <output name="listing"> - <assert_contents> - <has_line line="sample1.fasta" /> - <has_line line="other.fasta" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="fasta" file="sample1.fasta" /> - <element name="other" ftype="fasta" file="sample1.fasta" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="fasta"/> - <param name="results|start" value="sam" /> - <output name="listing"> - <assert_contents> - <has_line line="sample1.fasta" /> - <not_has_text text="other.fasta" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="fasta" file="sample1.fasta" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="fasta.gz"/> - <param name="results|last" value="le1" /> - <output name="listing"> - <assert_contents> - <has_line line="sample1.fasta" /> - <not_has_text text="other.fasta" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="fasta" file="sample1.fasta" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="fq"/> - <output name="listing"> - <assert_contents> - <has_line line="sample1.fastq" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="fastq" file="sample1.fastq" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="fastq"/> - <output name="listing"> - <assert_contents> - <has_line line="sample1.fastq" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="fastq" file="sample1.fastq" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="fastq"/> - <param name="results|extension|new_galaxy|new_ending" value="fastqsanger"/> - <output name="listing"> - <assert_contents> - <has_line line="sample1.fastqsanger" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="fastqsanger" file="sample1.fastq" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="fastq.gz"/> - <output name="data_collection"> - <assert_contents> - <has_line line="sample1.fastq" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="fastq" file="sample1.fastq" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="fastq.gz"/> - <param name="results|extension|new_galaxy|new_ending" value="fastqsanger"/> - <output name="listing_fastq_gz"> - <assert_contents> - <has_line line="sample1.fastqsanger" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="fastqsanger" file="sample1.fastq" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="sam"/> - <output name="listing"> - <assert_contents> - <has_line line="sample1.sam" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="sam" file="sample1.sam" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="tabular"/> - <output name="listing"> - <assert_contents> - <has_line line="sample1.tabular" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="tabular" file="sample1.tabular" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="text"/> - <output name="listing_text"> - <assert_contents> - <has_line line="sample1.txt" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="txt" file="sample1.text" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="tsv"/> - <output name="data_collection"> - <assert_contents> - <has_line line="sample1.tabular" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="tabular" file="sample1.tsv" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="txt" /> - <output name="listing"> - <assert_contents> - <has_line line="sample1.txt" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="txt" file="sample1.txt" /> - <element name="sample2" ftype="txt" file="sample2.txt" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="xls"/> - <output name="listing"> - <assert_contents> - <has_line line="sample1.xls" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="xls" file="sample1.xls" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|extension|file_type" value="xlsx"/> - <output name="listing"> - <assert_contents> - <has_line line="sample1.xlsx" /> - </assert_contents> - </output> - <output_collection name="data_collection" type="list"> - <element name="sample1" ftype="xlsx" file="sample1.xlsx" /> - </output_collection> - </test> - <test> - <param name="directory" value="test-data" /> - <param name="results|required" value="listing"/> - <output name="listing_all"> - <assert_contents> - <has_line line="sample1.csv" /> - <has_line line="sample1.fasta" /> - <has_line line="sample1.fasta.gz" /> - <has_line line="sample1.fastq" /> - <has_line line="sample1.fastq.gz" /> - <has_line line="sample1.sam" /> - <has_line line="sample1.tabular" /> - <has_line line="sample1.text" /> - <has_line line="sample1.tsv" /> - <has_line line="sample1.txt" /> - <has_line line="sample1.xls" /> - <has_line line="sample1.xlsx" /> - </assert_contents> - </output> - </test> - - </tests> - - <help> -<![CDATA[ -This tool will lookup files on the Galaxy server machine, including mounted directories. - -Only directories that are included in the white list and not in the black list are allowed. -If the directory you require does not pass the white list or blacklist test please contact the local galaxy admin. -(Admins see README) - -This tool only supports a limited set of types and file extenstions. -No other files are ever returned either by data or listing. -These endings are case senitive. - -==== - -The data options will look for all files that have a particular ending in the selected directory. - -The tool will return two things. - -1. A Dataset collection of all the detected files. - -2. A file with the names of all the detected files. These will be sorted in the same order as galaxy builds the dataset collection. - -The files can be filtered by setting a specific start strinf for the file name. -Only files that start with this string (case senstive) will be included. - -Files can also be filter for the last part before the file extsentions. - -Assuming the directory has: -C01_R1_001.fasta C01_R2_001.fatsa C02_R1_001.fasta C02_R2_001.fatsa - -Setting start C01 will return just the C01 files: C01_R1_001.fasta C01_R2_001.fatsa - -Setting last R1_001 will return the read1 files: C01_R1_001.fasta C02_R1_001.fasta - -As Galaxy detects the file type based on the extension this tool will change the exstension for supported alternative file ends. - This includes (manually) setting the exstension to fastqsanger, fastqsolexa, fastqillumina for tools that specify one of these. - -This tool will unzip gz files. - -==== - -The listing option will return a txt file with all the files found with any of the supported endings. Other files in that directory are not included. - -The file exstensions are left as in the directory. - -File start and last filters are not supported in this mode. -]]> - </help> - <citations> - </citations> - -</tool>