Mercurial > repos > iuc > colibread_commet

comparison macros.xml @ 4:8c53dc8b4adb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
author iuc
date Mon, 17 Aug 2020 10:38:36 -0400
parents 291753bf4013
children d03353742508
comparison
equal deleted inserted replaced
3:c53c11869b29 4:8c53dc8b4adb
1 <macros> 1 <macros>
2 <token name="@DISCOSNP_VERSION@">2.5.4</token>
3
2 <xml name="discosnp_requirements"> 4 <xml name="discosnp_requirements">
3 <requirements> 5 <requirements>
4 <requirement type="package" version="2.3.0">discosnp</requirement> 6 <requirement type="package" version="@DISCOSNP_VERSION@">discosnp</requirement>
5 </requirements> 7 </requirements>
6 </xml> 8 </xml>
7
8 <token name="@DISCOSNP_VERSION@">2.3.0</token>
9 9
10 <token name="@discosnp_single_reads@"><![CDATA[ 10 <token name="@discosnp_single_reads@"><![CDATA[
11 #for $input in $input_type_options.list_reads 11 #for $input in $input_type_options.list_reads
12 #set $filename = os.path.basename(str($input)) + "." + $input.ext 12 #set $filename = os.path.basename(str($input)) + "." + $input.ext
13 ln -sf '${input}' '${filename}' && 13 ln -sf '${input}' '${filename}' &&
62 <option value="auto"></option> 62 <option value="auto"></option>
63 <option value="custom"></option> 63 <option value="custom"></option>
64 </param> 64 </param>
65 <when value="auto" /> 65 <when value="auto" />
66 <when value="custom"> 66 <when value="custom">
67 <param argument="-c" type="text" label="Minimal coverage per read set" value="4" help="e.g. 4 / 4,5,17 / 4,auto,auto"/> 67 <param argument="-c" type="text" label="Minimal coverage per read set" value="3" help="e.g. 3 / 3,5,17 / 3,auto,auto"/>
68 </when> 68 </when>
69 </conditional> 69 </conditional>
70 70
71 <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" /> 71 <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" />
72 <param argument="-d" type="integer" label="Max number of errors per read" value="1" help="Max number of errors per read" /> 72 <param argument="-d" type="integer" label="Max number of errors per read" value="1" help="Max number of errors per read" />
73 73
74 </xml> 74 </xml>
75 75
76 <token name="@discosnp_inputs@"><![CDATA[ 76 <token name="@discosnp_inputs@"><![CDATA[
77 -r input.lst 77 -r input.lst
78 -b ${b}
79 -D ${D} 78 -D ${D}
80 -P ${P} 79 -P ${P}
81 ${low_complexity} 80 ${low_complexity}
82 -k ${k} 81 -k ${k}
83 82