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

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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
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equal deleted inserted replaced
5:84584664264c 6:35c00763cb5c
1 <tool id="gatk2_reduce_reads" name="Reduce Reads" version="@VERSION@.0"> 1 <tool id="gatk2_reduce_reads" name="Reduce Reads" version="@VERSION@.0">
2 <description>in BAM files</description> 2 <description>in BAM files</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 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" 11 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
11 #if str( $reference_source.input_bam.metadata.bam_index ) != "None": 12 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
28 --BQSR "${input_recal}" 29 --BQSR "${input_recal}"
29 #end if 30 #end if
30 --disable_bam_indexing 31 --disable_bam_indexing
31 ' 32 '
32 #include source=$standard_gatk_options# 33 #include source=$standard_gatk_options#
33 34
34 ##start analysis specific options 35 ##start analysis specific options
35 #if $analysis_param_type.analysis_param_type_selector == "advanced": 36 #if $analysis_param_type.analysis_param_type_selector == "advanced":
36 -p ' 37 -p '
37 #if $analysis_param_type.context_size.__str__.strip() != '': 38 #if $analysis_param_type.context_size.__str__.strip() != '':
38 --context_size $analysis_param_type.context_size 39 --context_size $analysis_param_type.context_size
88 <filter type="data_meta" key="dbkey" ref="input_bam" /> 89 <filter type="data_meta" key="dbkey" ref="input_bam" />
89 </options> 90 </options>
90 </param> 91 </param>
91 </when> 92 </when>
92 </conditional> 93 </conditional>
93 94
94 <expand macro="gatk_param_type_conditional" /> 95 <expand macro="gatk_param_type_conditional" />
95 96
96 <conditional name="analysis_param_type"> 97 <conditional name="analysis_param_type">
97 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> 98 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
98 <option value="basic" selected="True">Basic</option> 99 <option value="basic" selected="True">Basic</option>
99 <option value="advanced">Advanced</option> 100 <option value="advanced">Advanced</option>
100 </param> 101 </param>
134 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" /> 135 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
135 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> 136 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
136 </outputs> 137 </outputs>
137 <tests> 138 <tests>
138 <test> 139 <test>
139 <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" /> 140 <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" />
140 <param name="reference_source_selector" value="history" /> 141 <param name="reference_source_selector" value="history" />
141 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> 142 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
142 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" /> 143 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
143 <param name="gatk_param_type_selector" value="basic" /> 144 <param name="gatk_param_type_selector" value="basic" />
144 <param name="analysis_param_type_selector" value="basic" /> 145 <param name="analysis_param_type_selector" value="basic" />