annotate macros.xml @ 1:ef8be69b8e9e draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 108e83ea251bee3b952cb49ef758e69294608c1d
author rnateam
date Wed, 02 Jan 2019 10:17:46 -0500
parents 559e11a57c3e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
1 <macros>
1
ef8be69b8e9e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 108e83ea251bee3b952cb49ef758e69294608c1d
rnateam
parents: 0
diff changeset
2 <token name="@VERSION@">1.0.8</token>
0
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
3
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
4 <xml name="requirements">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
5 <requirements>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
6 <requirement type="package" version="@VERSION@">cmv</requirement>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
7 </requirements>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
8 </xml>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
9
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
10 <xml name="stdio">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
11 <stdio>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
12 <exit_code range="1:" />
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
13 </stdio>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
14 </xml>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
15
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
16 <xml name="version">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
17 <version_command>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
18 <![CDATA[
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
19 HMMV --version
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
20 ]]>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
21 </version_command>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
22 </xml>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
23
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
24 <xml name="common_parameters">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
25 <param name="alignment_filepath" type="data" format="stockholm" label="Input stockholm alignment" optional="true"/>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
26 <param name="output_format" type="select" label="Output format" help="pdf, svg, png, ps">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
27 <option value="pdf">pdf</option>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
28 <option value="svg">svg</option>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
29 <option value="png">png</option>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
30 <option value="ps">ps</option>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
31 </param>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
32 <param name="model_details" type="select" label="Specify visualization detail level." help="minimal,simple,detailed">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
33 <option value="minimal">minimal</option>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
34 <option value="simple">simple</option>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
35 <option value="detailed">detailed</option>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
36 </param>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
37 <param name="emission_layout" type="select" label="Specify layout of emission probabilites." help="score,probability,bar">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
38 <option value="score">score</option>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
39 <option value="probability">probability</option>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
40 <option value="bar">bar</option>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
41 </param>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
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)"/>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
43 <param argument="-c" type="float" value="2" label="Image scaling factor" help="Set uniform scaling factor for image size (Default: 2)"/>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
44 <param argument="-w" type="integer" value="100" label="Maximum image width" help="Set maximal width of result figure (Default: 100)" optional="true"/>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
45 <param argument="-n" type="integer" value="50" label="Stockholm alignment entries" help="Set cutoff for included stockholm alignment entries (Default: 50)" optional="true"/>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
46 </xml>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
47
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
48 <xml name="vis_output">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
49 <collection name="output_pdfs" type="list" label="${tool.name} on ${on_string}: output.pdfs">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
50 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.pdf" format="pdf"/>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
51 <filter>common['output_format'] == 'pdf'</filter>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
52 </collection>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
53 <collection name="output_svg" type="list" label="${tool.name} on ${on_string}: output.svgs">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
54 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.svg" format="svg"/>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
55 <filter>common['output_format'] == 'svg'</filter>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
56 </collection>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
57 <collection name="output_png" type="list" label="${tool.name} on ${on_string}: output.pngs">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
58 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.png" format="png"/>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
59 <filter>common['output_format'] == 'png'</filter>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
60 </collection>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
61 <collection name="output_ps" type="list" label="${tool.name} on ${on_string}: output.ps">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
62 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.ps" format="ps"/>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
63 <filter>common['output_format'] == 'ps'</filter>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
64 </collection>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
65 </xml>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
66
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
67 <token name="@COMMON_ARGS@">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
68 -d $common.model_details
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
69 -e $common.emission_layout
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
70 -n $common.n
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
71 -w $common.w
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
72 -c $common.c
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
73 -t $common.t
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
74 -f $common.output_format
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
75 #if $common.alignment_filepath
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
76 -s $common.alignment_filepath
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
77 #end if
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
78 </token>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
79
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
80 <xml name="citations">
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
81 <citations>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
82 <citation type="doi">10.1093/nar/gkt329</citation>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
83 </citations>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
84 </xml>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
85 </macros>
559e11a57c3e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c
rnateam
parents:
diff changeset
86