# HG changeset patch
# User brenninc
# Date 1462773984 14400
# Node ID 1d1b8eb0e6b76191505769ff45fccf0e62a195dd
# Parent  971629438ca4a748711c9f1d87e745ccb984fc5d
Deleted selected files

diff -r 971629438ca4 -r 1d1b8eb0e6b7 data_reader.xml
--- 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>