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comparison gemini_query.xml @ 3:87e5559c248e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
author iuc
date Fri, 07 Dec 2018 12:32:48 -0500
parents 9dc6c42486a1
children ff3597f6e01b
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2:9dc6c42486a1 3:87e5559c248e
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
2 <description>Querying the GEMINI database</description> 2 <description>Querying the GEMINI database</description>
3 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">query</token> 5 <token name="@BINARY@">query</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 @PROVIDE_ANNO_DATA@
13
12 gemini @BINARY@ 14 gemini @BINARY@
13 15
14 --in "${in}" 16 --in "${in}"
15 17
16 #if $gt_filter.strip(): 18 #set $multiline_sql_expr = $gt_filter
17 --gt-filter "${gt_filter}" 19 #set $cmdln_param = "--gt-filter"
18 #end if 20 @MULTILN_SQL_EXPR_TO_CMDLN@
19 21
20 #if $sample_filter.strip(): 22 #set $multiline_sql_expr = $sample_filter
21 --sample-filter "${sample_filter}" 23 #set $cmdln_param = "--sample-filter"
22 #end if 24 @MULTILN_SQL_EXPR_TO_CMDLN@
23 25
24 $show_samples 26 $show_samples
25 $show_families 27 $show_families
26 $family_wise 28 $family_wise
27 $header 29 $header
33 --min-kindreds $min_kindreds 35 --min-kindreds $min_kindreds
34 #end if 36 #end if
35 ##--format FORMAT Format of output (JSON, TPED or default) # we will take default for the time being 37 ##--format FORMAT Format of output (JSON, TPED or default) # we will take default for the time being
36 ## --sample-delim STRING The delimiter to be used with the --show-samples option. 38 ## --sample-delim STRING The delimiter to be used with the --show-samples option.
37 39
38 #if $q.strip(): 40 #set $multiline_sql_expr = $q
39 -q "${q}" 41 #set $cmdln_param = "-q"
40 #end if 42 @MULTILN_SQL_EXPR_TO_CMDLN@
41 43
42 "${ infile }" 44 "${ infile }"
43 > "${ outfile }" 45 > "${ outfile }"
44 ]]> 46 ]]>
45 </command> 47 </command>