Mercurial > repos > iuc > gemini_set_somatic
comparison gemini_macros.xml @ 4:7b031989ea12 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author | iuc |
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date | Fri, 14 Dec 2018 12:53:10 -0500 |
parents | ef9991a4a9a7 |
children | 991049484627 |
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3:ef9991a4a9a7 | 4:7b031989ea12 |
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1 <macros> | 1 <macros> |
2 <!-- gemini version to be used --> | |
3 <token name="@VERSION@">0.18.1</token> | |
4 <!-- minimal annotation files version required by this version of gemini --> | |
5 <token name="@DB_VERSION@">181</token> | |
6 | |
2 <xml name="requirements"> | 7 <xml name="requirements"> |
3 <requirements> | 8 <requirements> |
4 <requirement type="package" version="0.18.1">gemini</requirement> | 9 <requirement type="package" version="@VERSION@">gemini</requirement> |
5 <requirement type="package" version="0.2.6">tabix</requirement> | 10 <requirement type="package" version="0.2.6">tabix</requirement> |
6 <!-- for conda useage --> | 11 <!-- for conda useage --> |
7 <!--requirement type="package" version="1.3.1">htslib</requirement--> | 12 <!--requirement type="package" version="1.3.1">htslib</requirement--> |
8 <yield /> | 13 <yield /> |
9 </requirements> | 14 </requirements> |
21 <regex match="Exception:" /> | 26 <regex match="Exception:" /> |
22 </stdio> | 27 </stdio> |
23 </xml> | 28 </xml> |
24 | 29 |
25 <xml name="annotation_dir"> | 30 <xml name="annotation_dir"> |
26 <param name="annotation_databases" type="select" optional="True" label="Choose a gemini annotation database"> | 31 <param name="annotation_databases" type="select" label="Choose a gemini annotation source"> |
27 <options from_data_table="gemini_databases"> | 32 <options from_data_table="gemini_versioned_databases"> |
28 <filter type="sort_by" column="0" /> | 33 <filter type="sort_by" column="0" /> |
34 <filter type="static_value" column="2" value="@DB_VERSION@" /> | |
29 </options> | 35 </options> |
30 </param> | 36 </param> |
31 </xml> | 37 </xml> |
32 | 38 |
33 <xml name="add_header_column"> | 39 <xml name="add_header_column"> |
95 <add source="'" target="'"'"'" /> | 101 <add source="'" target="'"'"'" /> |
96 </mapping> | 102 </mapping> |
97 </sanitizer> | 103 </sanitizer> |
98 </xml> | 104 </xml> |
99 | 105 |
106 <token name="@PROVIDE_ANNO_DATA@"><![CDATA[ | |
107 mkdir gemini && | |
108 ln -s "${annotation_databases.fields.path}/gemini/data" gemini/data && | |
109 export GEMINI_CONFIG="${annotation_databases.fields.path}" && | |
110 ]]></token> | |
111 | |
100 <token name="@MULTILN_SQL_EXPR_TO_CMDLN@"> | 112 <token name="@MULTILN_SQL_EXPR_TO_CMDLN@"> |
101 #set $sql_expr = str($multiline_sql_expr).strip() | 113 #set $sql_expr = str($multiline_sql_expr).strip() |
102 #if str($sql_expr): | 114 #if str($sql_expr): |
103 #set $sql_expr = $sql_expr.replace('\r\n', '\n') | 115 #set $sql_expr = $sql_expr.replace('\r\n', '\n') |
104 #set $sql_expr = $sql_expr.replace('\r', '\n') | 116 #set $sql_expr = $sql_expr.replace('\r', '\n') |
151 </xml> | 163 </xml> |
152 | 164 |
153 <xml name="gt_pl_max"> | 165 <xml name="gt_pl_max"> |
154 <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" /> | 166 <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" /> |
155 </xml> | 167 </xml> |
156 <token name="@VERSION@">0.18.1</token> | |
157 | 168 |
158 <xml name="citations"> | 169 <xml name="citations"> |
159 <citations> | 170 <citations> |
160 <citation type="doi">10.1371/journal.pcbi.1003153</citation> | 171 <citation type="doi">10.1371/journal.pcbi.1003153</citation> |
161 <yield /> | 172 <yield /> |