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annotate variant_apply_recalibration.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 |
|---|---|
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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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1 <tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="@VERSION@.1"> |
| 0 | 2 <description></description> |
| 3 <macros> | |
| 4 <import>gatk2_macros.xml</import> | |
| 5 </macros> | |
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6
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" /> |
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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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7 <expand macro="version_command" /> |
| 0 | 8 <command interpreter="python"> |
| 9 gatk2_wrapper.py | |
| 10 --stdout "${output_log}" | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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11 #for $var_count, $variant in enumerate( $reference_source.input_variants ): |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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12 -d "--input:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}" |
| 0 | 13 #end for |
| 14 -p ' | |
| 15 @JAR_PATH@ | |
| 16 -T "ApplyRecalibration" | |
| 17 \$GATK2_SITE_OPTIONS | |
| 18 | |
| 19 @THREADS@ | |
| 20 | |
| 21 #if $reference_source.reference_source_selector != "history": | |
| 22 -R "${reference_source.ref_file.fields.path}" | |
| 23 #end if | |
| 24 --recal_file "${reference_source.input_recal}" | |
| 25 --tranches_file "${reference_source.input_tranches}" | |
| 26 --out "${output_variants}" | |
| 27 ' | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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28 |
| 0 | 29 #include source=$standard_gatk_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:
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changeset
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30 |
| 0 | 31 ##start analysis specific options |
| 32 -p ' | |
| 33 --mode "${mode}" | |
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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
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34 |
| 0 | 35 #for $ignore_filter in $ignore_filters: |
| 36 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector ) | |
| 37 #if $ignore_filter_name == "custom": | |
| 38 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name ) | |
| 39 #end if | |
| 40 --ignore_filter "${ignore_filter_name}" | |
| 41 #end for | |
| 42 --ts_filter_level "${ts_filter_level}" | |
| 43 ' | |
| 44 </command> | |
| 45 <inputs> | |
| 46 <conditional name="reference_source"> | |
| 47 <expand macro="reference_source_selector_param" /> | |
| 48 <when value="cached"> | |
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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
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49 <expand macro="input_variants" /> |
| 0 | 50 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" /> |
| 51 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" /> | |
| 52 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
| 53 <options from_data_table="gatk2_picard_indexes"> | |
| 54 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --> | |
| 55 </options> | |
| 56 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 57 </param> | |
| 58 </when> | |
| 59 <when value="history"> <!-- FIX ME!!!! --> | |
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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
|
60 <expand macro="input_variants" /> |
| 0 | 61 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" /> |
| 62 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" /> | |
| 63 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | |
| 64 </when> | |
| 65 </conditional> | |
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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
|
66 |
| 0 | 67 <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
|
68 |
| 0 | 69 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &lt;mode&gt;"> |
| 70 <option value="SNP" selected="True">SNP</option> | |
| 71 <option value="INDEL">INDEL</option> | |
| 72 <option value="BOTH">BOTH</option> | |
| 73 </param> | |
| 74 <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &lt;ignore_filter&gt;"> | |
| 75 <conditional name="ignore_filter_type"> | |
| 76 <param name="ignore_filter_type_selector" type="select" label="Filter Type"> | |
| 77 <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option> | |
| 78 <option value="LowQual" >LowQual</option> | |
| 79 <option value="custom" selected="True">Other</option> | |
| 80 </param> | |
| 81 <when value="custom"> | |
| 82 <param name="filter_name" type="text" value="" label="Filter name"/> | |
| 83 </when> | |
| 84 <when value="HARD_TO_VALIDATE" /> | |
| 85 <when value="LowQual" /> | |
| 86 </conditional> | |
| 87 </repeat> | |
| 88 <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &lt;ts_filter_level&gt;"/> | |
| 89 </inputs> | |
| 90 <outputs> | |
| 91 <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (Variants File)" /> | |
| 92 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
| 93 </outputs> | |
| 94 <tests> | |
| 95 <!-- ADD TESTS --> | |
| 96 </tests> | |
| 97 <help> | |
| 98 **What it does** | |
| 99 | |
| 100 Applies cuts to the input vcf file (by adding filter lines) to achieve the desired novel FDR levels which were specified during VariantRecalibration | |
| 101 | |
| 102 For more information on using the ApplyRecalibration module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantrecalibration_ApplyRecalibration.html>`_. | |
| 103 | |
| 104 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
| 105 | |
| 106 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
| 107 | |
| 108 ------ | |
| 109 | |
| 110 **Inputs** | |
| 111 | |
| 112 GenomeAnalysisTK: ApplyRecalibration accepts a variant input file, a recalibration file and a tranches file. | |
| 113 | |
| 114 | |
| 115 **Outputs** | |
| 116 | |
| 117 The output is in VCF format. | |
| 118 | |
| 119 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
| 120 | |
| 121 ------- | |
| 122 | |
| 123 **Settings**:: | |
| 124 | |
| 125 | |
| 126 recal_file The output recal file used by ApplyRecalibration | |
| 127 tranches_file The input tranches file describing where to cut the data | |
| 128 out The output filtered, recalibrated VCF file | |
| 129 ts_filter_level The truth sensitivity level at which to start filtering | |
| 130 ignore_filter If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file | |
| 131 mode Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously. (SNP|INDEL|BOTH) | |
| 132 | |
| 133 @CITATION_SECTION@ | |
| 134 </help> | |
| 4 | 135 <expand macro="citations" /> |
| 0 | 136 </tool> |