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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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0
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3 <command interpreter="python">
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1
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4 <![CDATA[
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0
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5 directory_copier.py
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1
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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 $results.start
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2
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12 --start "$results.start"
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1
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13 #end if
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14 #if $results.last
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2
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15 --last "$results.last"
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16 #end if
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17 #if $results.regex
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18 --regex "$results.regex"
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1
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19 #end if
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20 #end if
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21 --path ${directory.fields.path}
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22 --list ${listing}
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param name="directory" type="select" label="Directory to import data from">
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27 <options from_data_table="directory_data"/>
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28 <validator type="no_options" message="No Data Directory Setup"/>
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29 </param>
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0
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30 <param name="list_name" type="text" size="25" label="output name" value="input data"/>
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31 <conditional name="results">
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32 <param name="required" type="select" label="Download data or just directory listing" help="Select type of action required.">
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33 <option value="data" selected="true">Data and listing of selected type</option>
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34 <option value="listing">Get listing of selected file types </option>
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35 </param>
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36 <when value="data">
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37 <param name="start" type="text" value="" label="String which must be at the start of each file name" />
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38 <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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2
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39 <param name="regex" type="text" value="" label="Regex pattern which must somewhere in the file name (excluding the file type)" >
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40 <sanitizer>
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41 <valid initial="string.printable"/>
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42 </sanitizer>
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43 </param>
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0
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44 </when>
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45 <when value="listing"/>
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46 </conditional>
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47 </inputs>
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48 <outputs>
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49 <data format="txt" name="listing" label="List of files in $list_name">
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50 </data>
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51 <!-- Ideally galaxy can get the type based on the file extensions. If so just add the type here -->
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52 <collection type="list" label="$list_name" name="data_collection">
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53 <filter>(results['required'] == 'data')</filter>
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54 <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true" />
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55 </collection>
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56 </outputs>
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57 <tests>
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58 <test>
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1
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59 <param name="directory" value="fastq.gz_files_id" />
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60 <param name="list_name" value="test_files" />
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61 <param name="results|required" value="listing"/>
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0
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62 <output name="listing">
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63 <assert_contents>
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64 <has_line line="sample1.fastqsanger" />
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65 <has_line line="other.fastqsanger" />
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66 </assert_contents>
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67 </output>
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68 </test>
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69 <test>
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70 <param name="directory" value="fastq.gz_files_id" />
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0
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71 <output name="listing_fastq_gz">
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72 <assert_contents>
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73 <has_line line="sample1.fastqsanger" />
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74 </assert_contents>
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75 </output>
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76 <output_collection name="data_collection" type="list">
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77 <element name="sample1" ftype="fastqsanger" file="sample1.fastq" />
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1
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78 <element name="other" ftype="fastqsanger" file="other.fastq" />
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79 </output_collection>
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1
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80 </test>
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81 <test>
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82 <param name="directory" value="fastq_files_id" />
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83 <param name="results|start" value="sam" />
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84 <output name="listing_fastq">
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85 <assert_contents>
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86 <has_line line="sample1.fastq" />
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2
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87 <not_has_text text="other.fastq" />
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88 </assert_contents>
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89 </output>
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90 <output_collection name="data_collection" type="list">
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91 <element name="sample1" ftype="fastq" file="sample1.fastq" />
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92 </output_collection>
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93 </test>
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94 <test>
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95 <param name="directory" value="fastq_files_id" />
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96 <param name="results|regex" value="le.?" />
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97 <output name="listing_fastq">
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98 <assert_contents>
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99 <has_line line="sample1.fastq" />
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100 <not_has_text text="other.fastq" />
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0
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101 </assert_contents>
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102 </output>
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103 <output_collection name="data_collection" type="list">
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104 <element name="sample1" ftype="fastq" file="sample1.fastq" />
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105 </output_collection>
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1
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106 </test>
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107 </tests>
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108
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109 <help>
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110 <![CDATA[
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111 This tool will lookup files on the Galaxy server machine, including mounted directories.
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112
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113 Only directories and ending combinations set up by a Galaxy admin can be listed or loaded in this way.
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114 These endings are case senitive.
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115
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116 ====
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117
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118 The data options will look for all files that have a particular ending in the selected directory.
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119
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120 The tool will return two things.
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121
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122 1. A Dataset collection of all the detected files. (If data requested)
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123
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124 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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125
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126 The files can be filtered by setting a specific start string for the file name.
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127 Only files that start with this string (case senstive) will be included.
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128
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129 Files can also be filter for the last part before the file extsentions.
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130
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2
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131 Files can also be filtered by a regex pattern.
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132 Only files that contain the regex string will be included.
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133 This uses the python search funtion so as long as the Regex pattern is found somewhere in file name (excluding extension).
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134
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135 The three filter start, last and regex if supplied work indepently, so only files that pass all supplied test will be included.
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136
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137 Note: Before applying the last and regex test the ending (includig the . just before the ending are removed)
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138
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139 Assuming the directory has:
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140 C01_R1_001.fasta C01_R2_001.fatsa C02_R1_001.fasta C02_R2_002.fatsa
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141
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142 Setting start C01 will return just the C01 files: C01_R1_001.fasta C01_R2_002.fatsa
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143
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144 Setting last R1_001 will return the read1 files: C01_R1_001.fasta C02_R1_001.fasta
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145
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146 Setting regex R2_00.$ will return the R2 files: C01_R2_001.fatsa C02_R2_002.fatsa
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147
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148 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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149
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150 This tool will unzip gz files if requested to by the admin,
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151
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152 ]]>
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153 </help>
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154 <citations>
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155 </citations>
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156
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157 </tool>
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