diff data_reader.xml @ 1:1487421505f1 draft

Uploaded correct tool this time

--- a/data_reader.xml	Wed Mar 23 11:56:50 2016 -0400
+++ b/data_reader.xml	Wed Mar 23 12:08:33 2016 -0400
@@ -1,84 +1,29 @@
-<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>
+<tool id="directory_table_reader" name="Directory Data Reader" version="0.2">
+    <description>Reads data from preconfigured directories table.</description>
     <command interpreter="python">
-<![CDATA[
+        <![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 $results.last
+            --ending .${directory.fields.original_extension} 
+            --new_ending .${directory.fields.galaxy_extension} 
+            #if $results.required=="data"
+                --new_ending .${directory.fields.galaxy_extension} 
+                --decompress ${directory.fields.decompress} 
+                #if $results.start
+                    --start $results.start
+                #end if      
+                #if $results.last
+                    --last $results.last
+                #end if      
             #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}
-]]>
+            --path ${directory.fields.path} 
+            --list ${listing}
+        ]]>
     </command>
-    <macros>
-        <xml name="new_galaxy">
-            <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>
-        </xml>
-    </macros>    
     <inputs>
-        <param name="directory" type="text" label="Directory to read data from." />
+        <param name="directory" type="select" label="Directory to import data from">
+            <options from_data_table="directory_data"/>
+            <validator type="no_options" message="No Data Directory Setup"/>
+        </param>
         <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.">
@@ -88,51 +33,8 @@
             <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" >
-                        <expand macro="new_galaxy"/>
-                    </when>
-                    <when value="fastq.gz" >
-                        <expand macro="new_galaxy"/>
-                    </when>
-                    <when value="fq" >
-                        <expand macro="new_galaxy"/>
-                    </when>
-                    <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>
+            <when value="listing"/>
         </conditional>
     </inputs>
     <outputs>
@@ -146,113 +48,18 @@
     </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"/>
+            <param name="directory" value="fastq.gz_files_id" />
+            <param name="list_name" value="test_files" />
+            <param name="results|required" value="listing"/>
             <output name="listing">
                 <assert_contents>
                     <has_line line="sample1.fastqsanger" />
+                    <has_line line="other.fastqsanger" />
                 </assert_contents>
             </output>
-            <output_collection name="data_collection" type="list">
-                <element name="sample1" ftype="fastqsanger" file="sample1.fastq" />
-           </output_collection>
-        </test>
+         </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"/>
+            <param name="directory" value="fastq.gz_files_id" />
             <output name="listing_fastq_gz">
                 <assert_contents>
                     <has_line line="sample1.fastqsanger" />
@@ -260,126 +67,29 @@
             </output>
             <output_collection name="data_collection" type="list">
                 <element name="sample1" ftype="fastqsanger" file="sample1.fastq" />
+                <element name="other" ftype="fastqsanger" file="other.fastq" />
            </output_collection>
-        </test>
+         </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">
+            <param name="directory" value="fastq_files_id" />
+            <param name="results|start" value="sam" />
+            <output name="listing_fastq">
                 <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" />
+                    <has_line line="sample1.fastq" />
+                    <not_has_text text="other.fasta" />
                 </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" />
+                <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="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>
-
+         </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.
+Only directories and ending combinations set up by a Galaxy admin can be listed or loaded in this way.
 These endings are case senitive.
 
 ====
@@ -388,11 +98,11 @@
 
 The tool will return two things.
 
-1. A Dataset collection of all the detected files.
+1. A Dataset collection of all the detected files. (If data requested)
 
 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. 
+The files can be filtered by setting a specific start string 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.
@@ -404,18 +114,10 @@
 
 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.
+As Galaxy detects the file type based on the extension this tool will change the exstension as setup by the admin.
 
-====
-
-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.
+This tool will unzip gz files if requested to by the admin,
 
-The file exstensions are left as in the directory.
-
-File start and last filters are not supported in this mode.
 ]]>
     </help>
     <citations>