Mercurial > repos > iuc > gatk2

comparison variant_apply_recalibration.xml @ 6:35c00763cb5c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
5:84584664264c 6:35c00763cb5c
1 <tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="@VERSION@.0"> 1 <tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="@VERSION@.1">
2 <description></description> 2 <description></description>
3 <expand macro="requirements" />
4 <macros> 3 <macros>
5 <import>gatk2_macros.xml</import> 4 <import>gatk2_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
7 <command interpreter="python"> 8 <command interpreter="python">
8 gatk2_wrapper.py 9 gatk2_wrapper.py
9 --stdout "${output_log}" 10 --stdout "${output_log}"
10 #for $var_count, $variant in enumerate( $reference_source.variants ): 11 #for $var_count, $variant in enumerate( $reference_source.input_variants ):
11 -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}" 12 -d "--input:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}"
12 #end for 13 #end for
13 -p ' 14 -p '
14 @JAR_PATH@ 15 @JAR_PATH@
15 -T "ApplyRecalibration" 16 -T "ApplyRecalibration"
16 \$GATK2_SITE_OPTIONS 17 \$GATK2_SITE_OPTIONS
22 #end if 23 #end if
23 --recal_file "${reference_source.input_recal}" 24 --recal_file "${reference_source.input_recal}"
24 --tranches_file "${reference_source.input_tranches}" 25 --tranches_file "${reference_source.input_tranches}"
25 --out "${output_variants}" 26 --out "${output_variants}"
26 ' 27 '
27 28
28 #include source=$standard_gatk_options# 29 #include source=$standard_gatk_options#
29 30
30 ##start analysis specific options 31 ##start analysis specific options
31 -p ' 32 -p '
32 --mode "${mode}" 33 --mode "${mode}"
33 34
34 #for $ignore_filter in $ignore_filters: 35 #for $ignore_filter in $ignore_filters:
35 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector ) 36 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
36 #if $ignore_filter_name == "custom": 37 #if $ignore_filter_name == "custom":
37 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name ) 38 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name )
38 #end if 39 #end if
43 </command> 44 </command>
44 <inputs> 45 <inputs>
45 <conditional name="reference_source"> 46 <conditional name="reference_source">
46 <expand macro="reference_source_selector_param" /> 47 <expand macro="reference_source_selector_param" />
47 <when value="cached"> 48 <when value="cached">
48 <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;"> 49 <expand macro="input_variants" />
49 <param name="input_variants" type="data" format="vcf" label="Variant file to annotate"/>
50 </repeat>
51 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" /> 50 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
52 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" /> 51 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" />
53 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;"> 52 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
54 <options from_data_table="gatk2_picard_indexes"> 53 <options from_data_table="gatk2_picard_indexes">
55 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --> 54 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
56 </options> 55 </options>
57 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 56 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
58 </param> 57 </param>
59 </when> 58 </when>
60 <when value="history"> <!-- FIX ME!!!! --> 59 <when value="history"> <!-- FIX ME!!!! -->
61 <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;"> 60 <expand macro="input_variants" />
62 <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" />
63 </repeat>
64 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" /> 61 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
65 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" /> 62 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&amp;gt;" />
66 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" /> 63 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
67 </when> 64 </when>
68 </conditional> 65 </conditional>
69 66
70 <expand macro="gatk_param_type_conditional" /> 67 <expand macro="gatk_param_type_conditional" />
71 68
72 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;"> 69 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
73 <option value="SNP" selected="True">SNP</option> 70 <option value="SNP" selected="True">SNP</option>
74 <option value="INDEL">INDEL</option> 71 <option value="INDEL">INDEL</option>
75 <option value="BOTH">BOTH</option> 72 <option value="BOTH">BOTH</option>
76 </param> 73 </param>