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comparison variant_select.xml @ 13:669a23f1f4b5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit e5a5ad091c621348dc6ce2df861475ebc54a380e
author iuc
date Tue, 13 Oct 2015 17:22:38 -0400
parents 0d369d08ad6e
children
comparison
equal deleted inserted replaced
12:86007c982f00 13:669a23f1f4b5
1 <tool id="gatk2_variant_select" name="Select Variants" version="@VERSION@.0"> 1 <tool id="gatk2_variant_select" name="Select Variants" version="@VERSION@.2">
2 <description>from VCF files</description> 2 <description>from VCF files</description>
3 <macros> 3 <macros>
4 <import>gatk2_macros.xml</import> 4 <import>gatk2_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
48 #end for 48 #end for
49 49
50 ##start tool specific options 50 ##start tool specific options
51 #if str( $analysis_param_type.analysis_param_type_selector ) == 'advanced': 51 #if str( $analysis_param_type.analysis_param_type_selector ) == 'advanced':
52 -p ' 52 -p '
53 #for $exclude_sample_file in $analysis_param_type.exclude_sample_file_repeat: 53 #for $esf in $analysis_param_type.exclude_sample_file:
54 --exclude_sample_file "${exclude_sample_file.exclude_sample_file}" 54 --exclude_sample_file "${esf}"
55 #end for 55 #end for
56 56
57 #for $sample_file in $analysis_param_type.sample_file_repeat: 57 #for $sf in $analysis_param_type.sample_file:
58 --sample_file "${ample_file.sample_file}" 58 --sample_file "${sf}"
59 #end for 59 #end for
60 60
61 #if $analysis_param_type.input_keep_ids: 61 #if $analysis_param_type.input_keep_ids:
62 --keepIDs "${analysis_param_type.input_keep_ids}" 62 --keepIDs "${analysis_param_type.input_keep_ids}"
63 #end if 63 #end if
141 141
142 <expand macro="gatk_param_type_conditional" /> 142 <expand macro="gatk_param_type_conditional" />
143 143
144 <expand macro="analysis_type_conditional"> 144 <expand macro="analysis_type_conditional">
145 145
146 <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file" help="-xl_sf,--exclude_sample_file &amp;lt;exclude_sample_file&amp;gt;"> 146 <param name="exclude_sample_file" type="data" format="txt" multiple="True" label="Exclude Samples by file" help="File containing a list of samples (one per line) to exclude (-xl_sf,--exclude_sample_file &amp;lt;exclude_sample_file&amp;gt;)"/>
147 <param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/> 147
148 </repeat> 148 <param name="sample_file" type="data" format="txt" multiple="True" label="Samples by file" help="File containing a list of samples (one per line) to include (-sf,--sample_file &amp;lt;sample_file&amp;gt;)"/>
149 149
150 <repeat name="sample_file_repeat" title="Samples by file" help="-sf,--sample_file &amp;lt;sample_file&amp;gt;"> 150 <param name="input_keep_ids" type="data" format="txt" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &amp;lt;keepIDs&amp;gt;"/>
151 <param name="sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to include" />
152 </repeat>
153
154 <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &amp;lt;keepIDs&amp;gt;"/>
155 151
156 <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" help="-keepOriginalAC,--keepOriginalAC" /> 152 <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" help="-keepOriginalAC,--keepOriginalAC" />
157 153
158 <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" help="-mv,--mendelianViolation" /> 154 <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" help="-mv,--mendelianViolation" />
159 155