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