Mercurial > repos > iuc > hmmer_alimask

comparison alimask.xml @ 3:819d044451ed draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author iuc
date Sat, 07 Apr 2018 03:48:26 -0400
parents a20b2c7c5eee
children b4dc65565864
comparison
equal deleted inserted replaced
2:ebd48eca97bc 3:819d044451ed
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_alimask" name="alimask" version="@WRAPPER_VERSION@.0"> 2 <tool id="hmmer_alimask" name="alimask" version="@TOOL_VERSION@">
3 <description>append modelmask line to a multiple sequence alignments</description> 3 <description>append modelmask line to a multiple sequence alignments</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10
11 alimask 10 alimask
12 11
13 #if $range_type.range_type_select == "model": 12 #if $range_type.range_type_select == "model":
14 #set range = ','.join( [ "%s-%s" % (str($range.modelrangestart), str($range.modelrangeend)) for $range in $range_type.modelranges]) 13 #set range = ','.join( [ "%s-%s" % (str($range.modelrangestart), str($range.modelrangeend)) for $range in $range_type.modelranges])
15 --modelrange $range 14 --modelrange $range
21 @FORMAT_SELECTOR@ 20 @FORMAT_SELECTOR@
22 @MCSS@ 21 @MCSS@
23 @ARSWS@ 22 @ARSWS@
24 @SEED@ 23 @SEED@
25 24
26 $msafile 25 '$msafile'
27 $output 26 '$output'
28 ]]></command> 27 ]]></command>
29 <inputs> 28 <inputs>
30 <expand macro="input_msa" /> 29 <expand macro="input_msa" />
31 <conditional name="range_type"> 30 <conditional name="range_type">
32 <param name="range_type_select" type="select" 31 <param name="range_type_select" type="select"
33 label="Input range coordinate basis"> 32 label="Input range coordinate basis">
34 <option value="model">Range in model coordinates</option> 33 <option value="model">Range in model coordinates</option>
35 <option value="ali">Range in alignment coordinates</option> 34 <option value="ali">Range in alignment coordinates</option>
36 </param> 35 </param>
37 <when value="model"> 36 <when value="model">
38 <repeat min="1" name="modelranges" title="Model Ranges"> 37 <repeat name="modelranges" min="1" title="Model Ranges">
39 <param label="Model Range Start" name="modelrangestart" type="integer" value="10" /> 38 <param name="modelrangestart" type="integer" value="10" label="Model Range Start" />
40 <param label="Model Range End" name="modelrangeend" type="integer" value="20" /> 39 <param name="modelrangeend" type="integer" value="20" label="Model Range End" />
41 </repeat> 40 </repeat>
42 </when> 41 </when>
43 <when value="ali"> 42 <when value="ali">
44 <repeat min="1" name="aliranges" title="Alignment Ranges"> 43 <repeat name="aliranges" min="1" title="Alignment Ranges">
45 <param label="Alignment Range Start" name="alirangestart" type="integer" value="10" /> 44 <param name="alirangestart" type="integer" value="10" label="Alignment Range Start" />
46 <param label="Alignment Range End" name="alirangeend" type="integer" value="20" /> 45 <param name="alirangeend" type="integer" value="20" label="Alignment Range End" />
47 </repeat> 46 </repeat>
48 </when> 47 </when>
49 </conditional> 48 </conditional>
50 49
51 <!-- TODO: support model2ali/ali2model as separate utilities? --> 50 <!-- TODO: support model2ali/ali2model as separate utilities? -->
53 <expand macro="mcss"/> 52 <expand macro="mcss"/>
54 <expand macro="arsws"/> 53 <expand macro="arsws"/>
55 <expand macro="seed"/> 54 <expand macro="seed"/>
56 </inputs> 55 </inputs>
57 <outputs> 56 <outputs>
58 <data format="stockholm" name="output" label="Output MSA"/> 57 <data name="output" format="stockholm" label="Output MSA"/>
59 </outputs> 58 </outputs>
60 <tests> 59 <tests>
61 <test> 60 <test>
62 <param name="msafile" value="globins4.sto"/> 61 <param name="msafile" value="globins4.sto"/>
63 <param name="modelrangestart" value="10" /> 62 <param name="modelrangestart" value="10" />
108 @MCSS_HELP@ 107 @MCSS_HELP@
109 @ARSWS_HELP@ 108 @ARSWS_HELP@
110 @SEED_HELP@ 109 @SEED_HELP@
111 110
112 @ATTRIBUTION@ 111 @ATTRIBUTION@
113 ]]></help> 112 ]]></help>
114 <expand macro="citation"/> 113 <expand macro="citation"/>
115 </tool> 114 </tool>