|
0
|
1 <tool id="queue_genotype_workflow" name="Queue genotype workflow" version="1.0.0">
|
|
|
2 <description></description>
|
|
|
3 <command detect_errors="exit_code"><![CDATA[
|
|
|
4 #set history_id = $__app__.security.encode_id($affy_metadata.history.id)
|
|
|
5 python $__tool_directory__/queue_genotype_workflow.py
|
|
|
6 --affy_metadata '$affy_metadata'
|
|
|
7 --annot '$annot'
|
|
|
8 --api_key $get_user_api_key
|
|
|
9 --calls '$calls'
|
|
|
10 --confidences '$confidences'
|
|
|
11 --config_file $__tool_directory__/qgw_config.ini
|
|
|
12 --history_id $history_id
|
|
|
13 --reference_genome '$locally_cached_item.fields.path'
|
|
|
14 --dbkey '$locally_cached_item.fields.value'
|
|
|
15 --report '$report'
|
|
|
16 --sample_attributes '$sample_attributes'
|
|
|
17 --snp-posteriors '$snp_posteriors'
|
|
|
18 --summary '$summary'
|
|
|
19 --output '$output']]></command>
|
|
|
20 <configfiles>
|
|
|
21 <configfile name="get_user_api_key"><![CDATA[#from galaxy.managers import api_keys#${api_keys.ApiKeyManager( $__app__ ).get_or_create_api_key($__user__)} ]]></configfile>
|
|
|
22 </configfiles>
|
|
|
23 <inputs>
|
|
|
24 <param name="affy_metadata" type="data" format="tabular" label="Affymetrix 96 well plate metadata file" help="The word 'metadata' must be in the file name.">
|
|
2
|
25 <validator type="expression" message="96 well plate data must have 32 columns"><![CDATA[value is not None and value.metadata.columns==32]]></validator>
|
|
0
|
26 </param>
|
|
|
27 <param name="sample_attributes" type="data" format="tabular" label="Sample attributes file" help="The word 'attributes' must be in the file name."/>
|
|
|
28 <param name="annot" type="data" format="csv" label="Probeset annotation file" help="The word 'annotation' must be in the file name."/>
|
|
|
29 <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" help="The word 'summary' must be in the file name."/>
|
|
|
30 <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" help="The word 'snp-posteriors' must be in the file name."/>
|
|
|
31 <param name="report" type="data" format="txt" label="Apt-probeset genotype report file" help="The word 'report' must be in the file name."/>
|
|
|
32 <param name="confidences" type="data" format="txt" label="Apt-probeset genotype confidences file" help="The word 'confidences' must be in the file name."/>
|
|
|
33 <param name="calls" type="data" format="txt" label="Apt-probeset genotype calls file" help="The word 'calls' must be in the file name."/>
|
|
|
34 <param name="locally_cached_item" type="select" format="fasta" label="Fasta reference sequence">
|
|
|
35 <options from_data_table="all_fasta">
|
|
|
36 <column name="name" index="2"/>
|
|
|
37 <column name="value" index="0"/>
|
|
|
38 <column name="path" index="3"/>
|
|
|
39 <filter type="sort_by" column="1"/>
|
|
|
40 <validator type="no_options" message="No cached Fasta genome references are available for the build associated with the selected probeset annotation file." />
|
|
|
41 </options>
|
|
|
42 </param>
|
|
|
43 </inputs>
|
|
|
44 <outputs>
|
|
|
45 <data name="output" label="${tool.name} execution log" format="txt" />
|
|
|
46 </outputs>
|
|
|
47 <tests>
|
|
|
48 <test>
|
|
|
49 <!--Testing this tool is a bit difficult at the current time.-->
|
|
|
50 </test>
|
|
|
51 </tests>
|
|
|
52 <help>
|
|
|
53 **What it does**
|
|
|
54
|
|
5
|
55 Uses the Galaxy/Bioblend API to execute the complete multilocus genotype analysis pipeline for corals or symbionts.
|
|
0
|
56 This tool must be able to access the corals (stag) database.
|
|
|
57
|
|
3
|
58 **Required options**
|
|
|
59
|
|
|
60 * **Affymetrix 96 well plate metadata file** - a tabular file created by the user to describe their samples - it can be exported from Excel using this example as a template: http://baumslab.org/documents/SNPChip/STAG_Metadata_Template_v3.xlsm
|
|
|
61 * **Sample attributes file** - the Sample Attributes tabular file created by the Affymetrix sequencer for the plate
|
|
|
62 * **Probeset annotation file** - the annotation CSV file created by the Affymetrix sequencer for the plate
|
|
|
63 * **Apt-probeset genotype summary file** - the summary CSV file created by the Affymetrix sequencer for the plate
|
|
|
64 * **Apt-probeset genotype snp-posteriors file** - the snp-posteriors CSV file created by the Affymetrix sequencer for the plate
|
|
|
65 * **Apt-probeset genotype report file** - the report CSV file created by the Affymetrix sequencer for the plate
|
|
|
66 * **Apt-probeset genotype confidences file** - the confidences CSV file created by the Affymetrix sequencer for the plate
|
|
|
67 * **Apt-probeset genotype calls file** - the calls CSV file created by the Affymetrix sequencer for the plate
|
|
|
68 * **Fasta reference sequence** - selected fasta reference dataset for the samples
|
|
|
69
|
|
0
|
70 </help>
|
|
|
71 <citations>
|
|
|
72 <citation type="bibtex">
|
|
|
73 @misc{None,
|
|
|
74 journal = {None},
|
|
|
75 author = {Baums I},
|
|
|
76 title = {Manuscript in preparation},
|
|
|
77 year = {None},
|
|
|
78 url = {http://baumslab.org}
|
|
|
79 </citation>
|
|
|
80 </citations>
|
|
|
81 </tool>
|
|
|
82
|
