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comparison queue_genotype_workflow.xml @ 0:c80fae8c94c1 draft

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author greg
date Thu, 15 Aug 2019 11:17:33 -0400
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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.">
25 <validator type="expression" message="96 well plate data must have 32 columns and no more than 96 lines of data"><![CDATA[value is not None and value.metadata.columns==32 and value.metadata.data_lines<=96]]></validator>
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
55 Uses the Galaxy/Bioblend API to execute the complete multilocus genotype analysis pipeline for corals or symbiants.
56 This tool must be able to access the corals (stag) database.
57
58 </help>
59 <citations>
60 <citation type="bibtex">
61 @misc{None,
62 journal = {None},
63 author = {Baums I},
64 title = {Manuscript in preparation},
65 year = {None},
66 url = {http://baumslab.org}
67 </citation>
68 </citations>
69 </tool>
70