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