Mercurial > repos > greg > queue_genotype_workflow
comparison queue_genotype_workflow.xml @ 0:c80fae8c94c1 draft
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author | greg |
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date | Thu, 15 Aug 2019 11:17:33 -0400 |
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children | fa50d7c895c2 |
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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 |