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comparison data_reader.xml @ 8:288a172e95aa draft default tip

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author brenninc
date Mon, 09 May 2016 02:25:23 -0400
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7:1d1b8eb0e6b7 8:288a172e95aa
1 <tool id="directory_table_reader" name="Directory Data Reader" version="0.2">
2 <description>Reads data from preconfigured directories table.</description>
3 <command interpreter="python">
4 <![CDATA[
5 directory_copier.py
6 --ending .${directory.fields.original_extension}
7 --new_ending .${directory.fields.galaxy_extension}
8 #if $results.required=="data"
9 --new_ending .${directory.fields.galaxy_extension}
10 --decompress ${directory.fields.decompress}
11 #if $results.start
12 --start $results.start
13 #end if
14 #if $results.last
15 --last $results.last
16 #end if
17 #end if
18 --path ${directory.fields.path}
19 --list ${listing}
20 ]]>
21 </command>
22 <inputs>
23 <param name="directory" type="select" label="Directory to import data from">
24 <options from_data_table="directory_data"/>
25 <validator type="no_options" message="No Data Directory Setup"/>
26 </param>
27 <param name="list_name" type="text" size="25" label="output name" value="input data"/>
28 <conditional name="results">
29 <param name="required" type="select" label="Download data or just directory listing" help="Select type of action required.">
30 <option value="data" selected="true">Data and listing of selected type</option>
31 <option value="listing">Get listing of selected file types </option>
32 </param>
33 <when value="data">
34 <param name="start" type="text" value="" label="String which must be at the start of each file name" />
35 <param name="last" type="text" value="" label="String which must be at the end of the file name (excluding the file type)" />
36 </when>
37 <when value="listing"/>
38 </conditional>
39 </inputs>
40 <outputs>
41 <data format="txt" name="listing" label="List of files in $list_name">
42 </data>
43 <!-- Ideally galaxy can get the type based on the file extensions. If so just add the type here -->
44 <collection type="list" label="$list_name" name="data_collection">
45 <filter>(results['required'] == 'data')</filter>
46 <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true" />
47 </collection>
48 </outputs>
49 <tests>
50 <test>
51 <param name="directory" value="fastq.gz_files_id" />
52 <param name="list_name" value="test_files" />
53 <param name="results|required" value="listing"/>
54 <output name="listing">
55 <assert_contents>
56 <has_line line="sample1.fastqsanger" />
57 <has_line line="other.fastqsanger" />
58 </assert_contents>
59 </output>
60 </test>
61 <test>
62 <param name="directory" value="fastq.gz_files_id" />
63 <output name="listing_fastq_gz">
64 <assert_contents>
65 <has_line line="sample1.fastqsanger" />
66 </assert_contents>
67 </output>
68 <output_collection name="data_collection" type="list">
69 <element name="sample1" ftype="fastqsanger" file="sample1.fastq" />
70 <element name="other" ftype="fastqsanger" file="other.fastq" />
71 </output_collection>
72 </test>
73 <test>
74 <param name="directory" value="fastq_files_id" />
75 <param name="results|start" value="sam" />
76 <output name="listing_fastq">
77 <assert_contents>
78 <has_line line="sample1.fastq" />
79 <not_has_text text="other.fasta" />
80 </assert_contents>
81 </output>
82 <output_collection name="data_collection" type="list">
83 <element name="sample1" ftype="fastq" file="sample1.fastq" />
84 </output_collection>
85 </test>
86 </tests>
87
88 <help>
89 <![CDATA[
90 This tool will lookup files on the Galaxy server machine, including mounted directories.
91
92 Only directories and ending combinations set up by a Galaxy admin can be listed or loaded in this way.
93 These endings are case senitive.
94
95 ====
96
97 The data options will look for all files that have a particular ending in the selected directory.
98
99 The tool will return two things.
100
101 1. A Dataset collection of all the detected files. (If data requested)
102
103 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.
104
105 The files can be filtered by setting a specific start string for the file name.
106 Only files that start with this string (case senstive) will be included.
107
108 Files can also be filter for the last part before the file extsentions.
109
110 Assuming the directory has:
111 C01_R1_001.fasta C01_R2_001.fatsa C02_R1_001.fasta C02_R2_001.fatsa
112
113 Setting start C01 will return just the C01 files: C01_R1_001.fasta C01_R2_001.fatsa
114
115 Setting last R1_001 will return the read1 files: C01_R1_001.fasta C02_R1_001.fasta
116
117 As Galaxy detects the file type based on the extension this tool will change the exstension as setup by the admin.
118
119 This tool will unzip gz files if requested to by the admin,
120
121 ]]>
122 </help>
123 <citations>
124 </citations>
125
126 </tool>