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annotate variant_validate.xml @ 6:35c00763cb5c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
| author | iuc |
|---|---|
| date | Mon, 04 Jun 2018 05:38:15 -0400 |
| parents | f244b8209eb8 |
| children |
| rev | line source |
|---|---|
| 4 | 1 <tool id="gatk2_variant_validate" name="Validate Variants" version="@VERSION@.0"> |
| 0 | 2 <description></description> |
| 3 <macros> | |
| 4 <import>gatk2_macros.xml</import> | |
| 5 </macros> | |
|
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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changeset
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6 <expand macro="requirements" /> |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
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changeset
|
7 <expand macro="version_command" /> |
| 0 | 8 <command interpreter="python"> |
| 9 gatk2_wrapper.py | |
| 10 --stdout "${output_log}" | |
| 11 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" | |
| 12 -p ' | |
| 13 @JAR_PATH@ | |
| 14 -T "ValidateVariants" | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
15 |
| 0 | 16 \$GATK2_SITE_OPTIONS |
| 17 | |
| 18 #if $reference_source.reference_source_selector != "history": | |
| 19 -R "${reference_source.ref_file.fields.path}" | |
| 20 #end if | |
| 21 ${warn_on_errors} | |
| 22 ${do_not_validate_filtered_records} | |
| 23 ' | |
| 2 | 24 @DBSNP_OPTIONS@ |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
25 |
| 0 | 26 #include source=$standard_gatk_options# |
| 27 </command> | |
| 28 <inputs> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
29 |
| 0 | 30 <conditional name="reference_source"> |
| 31 <expand macro="reference_source_selector_param" /> | |
| 32 <when value="cached"> | |
| 33 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &lt;variant&gt;" /> | |
| 34 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
| 35 <options from_data_table="gatk2_picard_indexes"> | |
| 36 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> | |
| 37 </options> | |
| 38 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 39 </param> | |
| 40 </when> | |
| 41 <when value="history"> <!-- FIX ME!!!! --> | |
| 42 <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &lt;variant&gt;" /> | |
| 43 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | |
| 44 </when> | |
| 45 </conditional> | |
| 2 | 46 <expand macro="dbsnp_param" /> |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
47 |
| 0 | 48 <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen." help="-warnOnErrors,--warnOnErrors"/> |
| 49 <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed." help="-doNotValidateFilteredRecords,--doNotValidateFilteredRecords"/> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
50 |
| 0 | 51 <expand macro="gatk_param_type_conditional" /> |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
52 |
| 0 | 53 </inputs> |
| 54 <outputs> | |
| 55 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
| 56 </outputs> | |
| 57 <tests> | |
| 58 <test> | |
| 59 <param name="reference_source_selector" value="history" /> | |
| 60 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
| 61 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> | |
| 62 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" /> | |
| 63 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> | |
| 2 | 64 <param name="dbsnp_rod_name" value="dbsnp" /> |
| 0 | 65 <param name="warn_on_errors" value="True"/> |
| 66 <param name="do_not_validate_filtered_records" /> | |
| 67 <param name="gatk_param_type_selector" value="basic" /> | |
| 68 <output name="output_log" file="gatk/gatk_validate_variants/gatk_validate_variants_out_1.log.contains" compare="contains" /> | |
| 69 </test> | |
| 70 </tests> | |
| 71 <help> | |
| 72 **What it does** | |
| 73 | |
| 74 Validates a variants file. | |
| 75 | |
| 76 For more information on using the ValidateVariants module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_ValidateVariants.html>`_. | |
| 77 | |
| 78 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
| 79 | |
| 80 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
| 81 | |
| 82 ------ | |
| 83 | |
| 84 **Inputs** | |
| 85 | |
| 86 GenomeAnalysisTK: ValidateVariants accepts variant files as input. | |
| 87 | |
| 88 | |
| 89 **Outputs** | |
| 90 | |
| 91 The output is a log of variant validation. | |
| 92 | |
| 93 | |
| 94 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
| 95 | |
| 96 ------- | |
| 97 | |
| 98 **Settings**:: | |
| 99 | |
| 100 doNotValidateFilteredRecords should we skip validation on filtered records? | |
| 101 warnOnErrors should we just emit warnings on errors instead of terminating the run? | |
| 102 | |
| 103 @CITATION_SECTION@ | |
| 104 </help> | |
| 4 | 105 <expand macro="citations" /> |
| 0 | 106 </tool> |