|
0
|
1 <tool id="vl_import_data_sample" name="VLI.data_sample">
|
|
|
2 <description>import DataSample definitions within OMERO.biobank</description>
|
|
|
3 <command interpreter="bash">
|
|
|
4 launcher.sh
|
|
|
5 --interpreter=python
|
|
|
6 --runner=importer.py
|
|
|
7 #if $omero_configuration.level == 'advanced'
|
|
|
8 --host=$omero_configuration.vl_host
|
|
|
9 --user=$omero_configuration.vl_user
|
|
|
10 --passwd=$omero_configuration.vl_passwd
|
|
|
11 #else
|
|
|
12 --host=$__user_omero_host__
|
|
|
13 --user=$__user_omero_user__
|
|
|
14 --passwd=$__user_omero_password__
|
|
|
15 #end if
|
|
|
16 --operator=$__user_email__
|
|
|
17 --ifile=${input}
|
|
|
18 --ofile=${output}
|
|
|
19 --report_file=${report}
|
|
|
20 --logfile=${logfile}
|
|
|
21 #if $blocking_validation
|
|
|
22 --blocking-validator
|
|
|
23 #end if
|
|
|
24 data_sample
|
|
|
25 #if str($study) != 'use_provided'
|
|
|
26 --study ${study}
|
|
|
27 #end if
|
|
|
28 #if str($source_type) != 'use_provided'
|
|
|
29 --source-type=${source_type}
|
|
|
30 #end if
|
|
|
31 #if str($device_type) != 'use_provided'
|
|
|
32 --device-type=${device_type}
|
|
|
33 #end if
|
|
|
34 #if str($scanner) != 'use_provided'
|
|
|
35 --scanner=${scanner}
|
|
|
36 #end if
|
|
|
37 #if str($data_sample_type) != 'use_provided'
|
|
|
38 --data-sample-type=${data_sample_type}
|
|
|
39 #end if
|
|
|
40 </command>
|
|
|
41
|
|
|
42 <inputs>
|
|
|
43 <param format="tabular" name="input" type="data"
|
|
|
44 label="A tabular dataset with the following columns ..."/>
|
|
|
45
|
|
|
46 <param name="study" type="select" label="Context study" ajax = "True" ajax-source = "galaxy/get/studies" sort="True"
|
|
|
47 help="Choose from the already defined studies. See below.">
|
|
|
48 <option value="use_provided" selected="true">Records provide study labels</option>
|
|
|
49 </param>
|
|
|
50
|
|
|
51 <param name="source_type" type="select"
|
|
|
52 label="Type of the source"
|
|
|
53 help="Choose from the following. See below.">
|
|
|
54 <option value="use_provided" selected="true">
|
|
|
55 Use record provided
|
|
|
56 </option>
|
|
|
57 <option value="Individual">Individual</option>
|
|
|
58 <option value="Tube">Tube</option>
|
|
|
59 <option value="PlateWell">PlateWell</option>
|
|
|
60 <option value="DataSample">DataSample</option>
|
|
|
61 <option value="DataCollectionItem">DataCollectionItem</option>
|
|
|
62 <option value="IlluminaBeadChipArray">IlluminaBeadChipArray</option>
|
|
|
63 <option value="IlluminaBeadChipMeasures">IlluminaBeadChipMeasures</option>
|
|
|
64 </param>
|
|
|
65
|
|
|
66 <param name="device_type" type="select"
|
|
|
67 label="Type of the device"
|
|
|
68 help="Choose from the following. See below.">
|
|
|
69 <option value="use_provided" selected="true">
|
|
|
70 Use record provided</option>
|
|
|
71 <option value="Device">Device</option>
|
|
|
72 <option value="Chip">Chip</option>
|
|
|
73 <option value="SoftwareProgram">SoftwareProgram</option>
|
|
|
74 </param>
|
|
|
75
|
|
|
76
|
|
|
77 <param name="data_sample_type" type="select"
|
|
|
78 label="Type of the data sample"
|
|
|
79 help="Choose from the following. See below.">
|
|
|
80 <option value="use_provided" selected="true">
|
|
|
81 Use record provided</option>
|
|
|
82 <option value="GenotypeDataSample">GenotypeDataSample</option>
|
|
|
83 <option value="IlluminaBeadChipMeasure">IlluminaBeadChipMeasure</option>
|
|
|
84 <option value="GenomeVariationsDataSample">GenomeVariationsDataSample</option>
|
|
|
85 </param>
|
|
|
86
|
|
|
87 <param name="scanner" type="select" label="Scanner used" ajax = "True" ajax-source = "galaxy/get/scanners" sort="True"
|
|
|
88 help="Choose from the possible scanners. See below.">
|
|
|
89 <option value="use_provided" selected="true">Records provide scanner ids</option>
|
|
|
90 </param>
|
|
|
91
|
|
|
92 <!-- ************************************************** -->
|
|
|
93 <param name="blocking_validation" type="boolean" checked="false"
|
|
|
94 label="Blocking validation"
|
|
|
95 help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/>
|
|
|
96
|
|
|
97 <conditional name="wait_for_trigger">
|
|
|
98 <param name="enable_trigger" type="boolean" checked="false"
|
|
|
99 label="Wait for another tool to end before running this tool"/>
|
|
|
100 <when value="true">
|
|
|
101 <param format="txt" name="trigger_file" type="data"
|
|
|
102 label="Select the LOG file that will be used as trigger"/>
|
|
|
103 </when>
|
|
|
104 </conditional>
|
|
|
105
|
|
|
106 <conditional name="omero_configuration">
|
|
|
107 <param name="level" type="select" label="Configuration level">
|
|
|
108 <option value="default" selected="true">Default: use Galaxy's preferences</option>
|
|
|
109 <option value="advanced">Advanced: specify different host, user
|
|
|
110 and password</option>
|
|
|
111 </param>
|
|
|
112 <when value="default"/>
|
|
|
113 <when value="advanced">
|
|
|
114 <param name="vl_host" size="40" type="text" value="hostname"
|
|
|
115 label="OMERO.biobank host"/>
|
|
|
116 <param name="vl_user" size="40" type="text" value="user"
|
|
|
117 label="OMERO.biobank user"/>
|
|
|
118 <param name="vl_passwd" size="40" type="text" value="password"
|
|
|
119 label="OMERO.biobank passwd"/>
|
|
|
120 </when>
|
|
|
121 </conditional>
|
|
|
122
|
|
|
123 </inputs>
|
|
|
124
|
|
|
125 <outputs>
|
|
|
126 <data format="tabular" name="output" label="${tool.name}.mapping"/>
|
|
|
127 <data format="tabular" name="report" label="${tool.name}.report"/>
|
|
|
128 <data format="txt" name="logfile" label="${tool.name}.logfile"/>
|
|
|
129 </outputs>
|
|
|
130
|
|
|
131 <stdio>
|
|
|
132 <exit_code range="1:" level="fatal" />
|
|
|
133 </stdio>
|
|
|
134
|
|
|
135 <help>
|
|
|
136 Will read in a tsv file with the following columns::
|
|
|
137
|
|
|
138 study label source device device_type scanner options
|
|
|
139 ASTUDY foo01 v03909 v9309 Chip v99020 celID=0009099090
|
|
|
140 ASTUDY foo02 v03909 v99022 Scanner v99022 conf1=...,conf2=...
|
|
|
141 ....
|
|
|
142
|
|
|
143 In this example, the first line corresponds to a dataset obtained by
|
|
|
144 using chip v9309 on scanner v99020, while the second datasample has
|
|
|
145 been obtained using a technology directly using a scanner, e.g., an
|
|
|
146 Illumina HiSeq 2000. The '''scanner''' column is there as a
|
|
|
147 convenience to support a more detailed description of a chip-based
|
|
|
148 acquisition.
|
|
|
149
|
|
|
150 The general strategy is to decide what data objects should be
|
|
|
151 instantiated by looking at the chip column and at its corresponding
|
|
|
152 maker,model,release.
|
|
|
153
|
|
|
154 The optional column '''scanner''', the vid of the scanner device, is
|
|
|
155 used in cases, such as Affymetrix genotyping, where it is relevant.
|
|
|
156
|
|
|
157 It is also possible to import DataSample(s) that are the results of
|
|
|
158 processing other DataSample(s). Here is an example::
|
|
|
159
|
|
|
160 study label source device device_type options
|
|
|
161 ASTUDY foo01 v03909 v99021 SoftwareProgram conf1=...,conf2=...
|
|
|
162 ASTUDY foo02 v03909 v99021 SoftwareProgram conf1=...,conf2=...
|
|
|
163 ....
|
|
|
164 </help>
|
|
|
165 </tool>
|
