Mercurial > repos > iuc > bcftools_annotate

comparison bcftools_annotate.xml @ 5:eb782a60fc53 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author iuc
date Thu, 13 Apr 2017 17:44:38 -0400
parents 7b10a015526e
children 6a88248893c4
comparison
equal deleted inserted replaced
4:7b10a015526e 5:eb782a60fc53
32 #elif $section.annofile.header_lines: 32 #elif $section.annofile.header_lines:
33 #set $annotation_hdr = 'annotation.hdr' 33 #set $annotation_hdr = 'annotation.hdr'
34 grep '^\#\#INFO' ${hdr_file} > $annotation_hdr && 34 grep '^\#\#INFO' ${hdr_file} > $annotation_hdr &&
35 #end if 35 #end if
36 #end if 36 #end if
37 #set $section = $sec_restrict
37 38
38 bcftools @EXECUTABLE@ 39 bcftools @EXECUTABLE@
40 @PREPARE_REGIONS_FILE@
39 41
40 #set $section = $sec_annofile 42 #set $section = $sec_annofile
41 @COLUMNS@ 43 @COLUMNS@
42 #if $annotation_file: 44 #if $annotation_file:
43 --annotations "${annotation_file}" 45 --annotations "${annotation_file}"
63 65
64 ## Default section 66 ## Default section
65 #set $section = $sec_restrict 67 #set $section = $sec_restrict
66 @INCLUDE@ 68 @INCLUDE@
67 @EXCLUDE@ 69 @EXCLUDE@
70 @COLLAPSE@
68 @REGIONS@ 71 @REGIONS@
69 @SAMPLES@ 72 @SAMPLES@
70 73
71 @OUTPUT_TYPE@ 74 @OUTPUT_TYPE@
72 @THREADS@ 75 @THREADS@
73 76
74 ## Primary Input/Outputs 77 ## Primary Input/Outputs
75 @INPUT_FILE@ 78 @INPUT_FILE@
76 > "$output_file" 79 > '$output_file'
77 ]]> 80 ]]>
78 </command> 81 </command>
79 <configfiles> 82 <configfiles>
80 <configfile name="hdr_file"><![CDATA[#slurp 83 <configfile name="hdr_file"><![CDATA[#slurp
81 #if $sec_annofile.annofile.anno_fmt == 'tab' and str($sec_annofile.annofile.header_lines) != '': 84 #if $sec_annofile.annofile.anno_fmt == 'tab' and str($sec_annofile.annofile.header_lines) != '':
141 help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." /> 144 help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." />
142 </section> 145 </section>
143 <section name="sec_restrict" expanded="false" title="Restrict to"> 146 <section name="sec_restrict" expanded="false" title="Restrict to">
144 <expand macro="macro_include" /> 147 <expand macro="macro_include" />
145 <expand macro="macro_exclude" /> 148 <expand macro="macro_exclude" />
149 <expand macro="macro_collapse" />
146 <expand macro="macro_regions" /> 150 <expand macro="macro_regions" />
147 <expand macro="macro_samples" /> 151 <expand macro="macro_samples" />
148 </section> 152 </section>
149 <expand macro="macro_select_output_type" /> 153 <expand macro="macro_select_output_type" />
150 </inputs> 154 </inputs>