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comparison macros.xml @ 0:fccb17c9e7ef draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
author rnateam
date Fri, 20 Oct 2017 04:31:43 -0400
parents
children 8405fa59c2b2
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-1:000000000000 0:fccb17c9e7ef
1 <macros>
2 <token name="@VERSION@">1.0.6</token>
3
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@VERSION@">cmv</requirement>
7 </requirements>
8 </xml>
9
10 <xml name="stdio">
11 <stdio>
12 <exit_code range="1:" />
13 </stdio>
14 </xml>
15
16 <xml name="version">
17 <version_command>
18 <![CDATA[
19 HMMV --version
20 ]]>
21 </version_command>
22 </xml>
23
24 <xml name="common_parameters">
25 <param name="alignment_filepath" type="data" format="stockholm" label="Input stockholm alignment" optional="true"/>
26 <param name="output_format" type="select" label="Output format" help="pdf, svg, png, ps">
27 <option value="pdf">pdf</option>
28 <option value="svg">svg</option>
29 <option value="png">png</option>
30 <option value="ps">ps</option>
31 </param>
32 <param name="model_details" type="select" label="Specify visualization detail level." help="minimal,simple,detailed">
33 <option value="minimal">minimal</option>
34 <option value="simple">simple</option>
35 <option value="detailed">detailed</option>
36 </param>
37 <param name="emission_layout" type="select" label="Specify layout of emission probabilites." help="score,probability,bar">
38 <option value="score">score</option>
39 <option value="probability">probability</option>
40 <option value="bar">bar</option>
41 </param>
42 <param argument="-t" type="float" value="0.01" label="Transition probability threshold" help="Minimal value for a transition probability to be displayed (Default: 0.01)"/>
43 <param argument="-c" type="float" value="2" label="Image scaling factor" help="Set uniform scaling factor for image size (Default: 2)"/>
44 <param argument="-w" type="integer" value="100" label="Maximum image width" help="Set maximal width of result figure (Default: 100)" optional="true"/>
45 <param argument="-n" type="integer" value="50" label="Stockholm alignment entries" help="Set cutoff for included stockholm alignment entries (Default: 50)" optional="true"/>
46 </xml>
47
48 <xml name="vis_output">
49 <collection name="output_pdfs" type="list" label="${tool.name} on ${on_string}: output.pdfs">
50 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.pdf" format="pdf"/>
51 <filter>common['output_format'] == 'pdf'</filter>
52 </collection>
53 <collection name="output_svg" type="list" label="${tool.name} on ${on_string}: output.svgs">
54 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.svg" format="svg"/>
55 <filter>common['output_format'] == 'svg'</filter>
56 </collection>
57 <collection name="output_png" type="list" label="${tool.name} on ${on_string}: output.pngs">
58 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.png" format="png"/>
59 <filter>common['output_format'] == 'png'</filter>
60 </collection>
61 <collection name="output_ps" type="list" label="${tool.name} on ${on_string}: output.ps">
62 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.ps" format="ps"/>
63 <filter>common['output_format'] == 'ps'</filter>
64 </collection>
65 </xml>
66
67 <token name="@COMMON_ARGS@">
68 -d $common.model_details
69 -e $common.emission_layout
70 -n $common.n
71 -w $common.w
72 -c $common.c
73 -t $common.t
74 -f $common.output_format
75 #if $common.alignment_filepath
76 -s $common.alignment_filepath
77 #end if
78 </token>
79
80 <xml name="citations">
81 <citations>
82 <citation type="doi">10.1093/nar/gkt329</citation>
83 </citations>
84 </xml>
85 </macros>
86