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comparison gatk_macros.xml @ 0:b80ff7f43ad1 draft default tip

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planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
author avowinkel
date Thu, 24 Sep 2015 12:10:01 -0400
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-1:000000000000 0:b80ff7f43ad1
1 <macros>
2
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package">gatk</requirement>
6 <requirement type="set_environment">GATK_PATH</requirement>
7 <requirement type="set_environment">GATK_SITE_OPTIONS</requirement>
8 <requirement type="package" version="3.1.2.1">package_r_for_gatk_3_4_0</requirement>
9 </requirements>
10 </xml>
11
12 <xml name="version_command">
13 <version_command><![CDATA[ @GATK_EXEC@ --help|grep '^The Genome' ]]></version_command>
14 </xml>
15
16 <token name="@VERSION@">3.4-0</token>
17 <token name="@OUTPUT_NAME_PREFIX@">${tool.name} - ${analysis_type.analysis_type_selector}</token>
18 <token name="@GATK_EXEC@">
19 <![CDATA[
20 #if $cond_threads.cond_threads_enabled:
21 #if int($cond_threads.nct) > 1:
22 THREAD_STRING="-nct $cond_threads.nct" &&
23 #end if
24 #if int($cond_threads.nt) > 1:
25 THREAD_STRING=$THREAD_STRING" -nt $cond_threads.nt" &&
26 #end if
27 #if int($cond_threads.mem) > 0:
28 GATK_MEM=$cond_threads.mem &&
29 #end if
30 #end if
31 java -Xmx\${GATK_MEM:-\${SLURM_MEM_PER_NODE:-4096}}M -jar "\$GATK_PATH/GenomeAnalysisTK.jar" \${THREAD_STRING:-}
32 ]]>
33 </token>
34
35 <xml name="macro_vcf_input" tokens="tag">
36 <param name="input" type="data" format="vcf" multiple="true" label="Variant files (VCF format)" help="-V, &#8209;&#8209;variant">
37 <validator type="unspecified_build" />
38 <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." />
39 </param>
40 </xml>
41 <token name="@token_vcf_input_pre@" tokens="tag">
42 <![CDATA[
43 ############################
44 ## create links to gVCF input files with correct extensions
45 ############################
46 #for $i, $variant in enumerate($analysis_type.input):
47 ln -s -f ${variant} variant_${i}.vcf &&
48 #end for
49 ]]>
50 </token>
51 <token name="@token_vcf_input@">
52 <![CDATA[
53 #for $i, $variant in enumerate($analysis_type.input):
54 --variant variant_${i}.vcf
55 #end for
56 @token_reference_input@
57 ]]>
58 </token>
59
60
61 <xml name="macro_gvcf_input" tokens="tag">
62 <param name="input" type="data" format="vcf" multiple="true" label="Variant files (gVCF format)" help="-V, &#8209;&#8209;variant">
63 <validator type="unspecified_build" />
64 <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." />
65 </param>
66 </xml>
67 <token name="@token_gvcf_input_pre@" tokens="tag">
68 <![CDATA[
69 ############################
70 ## create links to gVCF input files with correct extensions
71 ############################
72 #for $i, $variant in enumerate($analysis_type.input):
73 ln -s -f ${variant} variant_${i}.g.vcf &&
74 #end for
75 ]]>
76 </token>
77 <token name="@token_gvcf_input@">
78 <![CDATA[
79 #for $i, $variant in enumerate($analysis_type.input):
80 --variant variant_${i}.g.vcf
81 #end for
82 @token_reference_input@
83 ]]>
84 </token>
85
86 <xml name="macro_bam_input">
87 <conditional name="cond_bam_input">
88 <param name="all_in_one" type="boolean" value="false" label="Input all BAM files in a single command" />
89 <when value="true">
90 <param name="input" type="data" format="bam" multiple="true" label="Input file containing sequence data (BAM)" help="-I, ‑‑input_file">
91 <validator type="unspecified_build"/>
92 <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build."/>
93 </param>
94 </when>
95 <when value="false">
96 <param name="input" type="data" format="bam" label="Input file containing sequence data (BAM)" help="-I, ‑‑input_file">
97 <validator type="unspecified_build"/>
98 <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build."/>
99 </param>
100 </when>
101 </conditional>
102 </xml>
103 <token name="@token_bam_input_pre@">
104 <![CDATA[
105 ############################
106 ## create links to bam input files with correct extensions
107 ############################
108 #if $analysis_type.cond_bam_input.all_in_one
109 #for $i, $bam in enumerate($analysis_type.cond_bam_input.input):
110 ln -s -f ${bam} input_${i}.bam &&
111 ln -s -f ${bam.metadata.bam_index} input_${i}.bam.bai &&
112 #end for
113 #else
114 ln -s -f ${analysis_type.cond_bam_input.input} input.bam &&
115 ln -s -f ${analysis_type.cond_bam_input.input.metadata.bam_index} input.bam.bai &&
116 #end if
117 ]]>
118 </token>
119 <token name="@token_bam_input@">
120 <![CDATA[
121 #if $analysis_type.cond_bam_input.all_in_one
122 #for $i, $bam in enumerate($analysis_type.cond_bam_input.input):
123 --input_file input_${i}.bam
124 #end for
125 #else
126 --input_file input.bam
127 #end if
128 @token_reference_input@
129 ]]>
130 </token>
131
132 <token name="@token_reference_input@">
133 <![CDATA[
134 ]]>
135 </token>
136 <xml name="macro_input" tokens="tag">
137 <yield />
138 </xml>
139
140 <xml name="macro_optional_parameters">
141 <conditional name="optional_parameters">
142 <param name="optional_parameters_enabled" type="boolean" label="Configure Optional Parameters" />
143 <when value="true">
144 <yield />
145 </when>
146 <when value="false" />
147 </conditional>
148 </xml>
149
150 <xml name="macro_advanced_parameters">
151 <conditional name="advanced_parameters">
152 <param name="advanced_parameters_enabled" type="boolean" label="Configure Advanced Parameters" />
153 <when value="true">
154 <yield />
155 </when>
156 <when value="false" />
157 </conditional>
158 </xml>
159
160 <xml name="macro_tests">
161 <tests>
162
163 </tests>
164 </xml>
165
166 </macros>