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comparison bwa_macros.xml @ 6:09a7281d24c5 draft

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planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Tue, 21 Jul 2015 14:12:49 -0400
parents fbf460831036
children d8c9597bfb09
comparison
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5:fbf460831036 6:09a7281d24c5
12 #set $rg_string += $format_read_group("\tKS:", $rg_ks) 12 #set $rg_string += $format_read_group("\tKS:", $rg_ks)
13 #set $rg_string += $format_read_group("\tPG:", $rg_pg) 13 #set $rg_string += $format_read_group("\tPG:", $rg_pg)
14 #set $rg_string += $format_read_group("\tPI:", $rg_pi) 14 #set $rg_string += $format_read_group("\tPI:", $rg_pi)
15 #set $rg_string += $format_read_group("\tPU:", $rg_pu) 15 #set $rg_string += $format_read_group("\tPU:", $rg_pu)
16 </token> 16 </token>
17 17
18 <xml name="stdio">
19 <stdio>
20 <exit_code range="1:" />
21 <exit_code range=":-1" />
22 <regex match="Error:" />
23 <regex match="Exception:" />
24 </stdio>
25 </xml>
26
27 <macro name="dbKeyActionsBwa">
28 <expand macro="dbKeyActions">
29 <option type="from_data_table" name="bwa_indexes" column="1" offset="0">
30 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
31 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
32 </option>
33 </expand>
34 </macro>
35
36 <macro name="dbKeyActionsBwaMem">
37 <expand macro="dbKeyActions">
38 <option type="from_data_table" name="bwa_mem_indexes" column="1" offset="0">
39 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
40 <filter type="param_value" ref="reference_source.ref_file" column="0"/>
41 </option>
42 </expand>
43 </macro>
44
45 <macro name="dbKeyActions">
46 <actions>
47 <conditional name="reference_source.reference_source_selector">
48 <when value="cached">
49 <action type="metadata" name="dbkey">
50 <yield />
51 </action>
52 </when>
53 <when value="history">
54 <action type="metadata" name="dbkey">
55 <option type="from_param" name="reference_source.ref_file" param_attribute="dbkey" />
56 </action>
57 </when>
58 </conditional>
59 </actions>
60 </macro>
61
18 <token name="@RG@"> 62 <token name="@RG@">
19 ----- 63 -----
20 64
21 .. class:: warningmark 65 .. class:: warningmark
22 66