Mercurial > repos > yhoogstrate > segmentation_fold

annotate segmentation-fold.xml @ 11:487f438da099 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c
author yhoogstrate
date Fri, 06 May 2016 05:45:36 -0400
parents 312edff152eb
children 63156f020cd3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
487f438da099 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c
yhoogstrate
parents: 10
diff changeset
1 <tool id="segmentation_fold" name="segmentation-fold" version="@VERSION@-1">
0
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
2 <description>RNA-Folding including predefined segments including K-turns</description>
11
487f438da099 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c
yhoogstrate
parents: 10
diff changeset
3 <macros>
487f438da099 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c
yhoogstrate
parents: 10
diff changeset
4 <import>macros.xml</import>
487f438da099 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c
yhoogstrate
parents: 10
diff changeset
5 </macros>
0
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
6
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
7 <requirements>
11
487f438da099 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c
yhoogstrate
parents: 10
diff changeset
8 @VERSION_COMMAND_SMF@
0
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
9 </requirements>
11
487f438da099 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c
yhoogstrate
parents: 10
diff changeset
10 <expand macro="stdio" />
0
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
11
11
487f438da099 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c
yhoogstrate
parents: 10
diff changeset
12 <version_command>@VERSION_COMMAND_SMF@</version_command>
0
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
13
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
14 <command><![CDATA[
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
15 segmentation-fold
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
16
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
17 #if $input.method == "fasta"
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
18 -f $input.input_fasta
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
19 #else
3
59ab674be4b5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 4b12ac5efae0802d2614747a639475d8778a68b4-dirty
yhoogstrate
parents: 2
diff changeset
20 -s $input.input_sequence
0
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
21 #end if
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
22
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
23 -p $predict_segments
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
24 -h $min_hairpin_size
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
25
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
26 #if $parameters.settings == "default"
3
59ab674be4b5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 4b12ac5efae0802d2614747a639475d8778a68b4-dirty
yhoogstrate
parents: 2
diff changeset
27 -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
0
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
28 #else
3
59ab674be4b5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 4b12ac5efae0802d2614747a639475d8778a68b4-dirty
yhoogstrate
parents: 2
diff changeset
29 -x "${parameters.input_xml}"
0
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
30 #end if
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
31
2
eccb5ee89df7 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36-dirty
yhoogstrate
parents: 0
diff changeset
32 -t \${GALAXY_SLOTS:-4}
0
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
33 > $output_dbn
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
34 ]]></command>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
35
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
36 <inputs>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
37 <conditional name="input">
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
38 <param name="method" type="select" label="Energy parameters">
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
39 <option value="fasta" selected="true">As FASTA-file</option>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
40 <option value="text">As text</option>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
41 </param>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
42 <when value="fasta">
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
43 <param name="input_fasta" type="data" format="fasta" label="Fasta file with RNA-sequece (-f)" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
44 </when>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
45 <when value="text">
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
46 <param name="input_sequence" type="text" label="RNA-sequece (-s)" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
47 </when>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
48 </conditional>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
49
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
50 <param name="predict_segments" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Enable segment prediction functionality (-p)" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
51 <param name="min_hairpin_size" type="integer" min="1" value="3" label="Minimum hairpin size (-h)" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
52
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
53 <conditional name="parameters">
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
54 <param name="settings" type="select" label="Energy parameters">
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
55 <option value="default" selected="true">Default</option>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
56 <option value="custom">Custom</option>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
57 </param>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
58 <when value="default" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
59 <when value="custom">
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
60 <param name="input_xml" type="data" format="xml" multiple="false" label="Use custom 'segments.xml'-syntaxed file (-x)" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
61 </when>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
62 </conditional>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
63 </inputs>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
64
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
65 <outputs>
7
bff6e82064da planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 4a09ba36d8feeea3b61ab5b2b113aac7f34d389f-dirty
yhoogstrate
parents: 5
diff changeset
66 <data format="dbn" name="output_dbn" label="segmentation-fold" />
3
59ab674be4b5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 4b12ac5efae0802d2614747a639475d8778a68b4-dirty
yhoogstrate
parents: 2
diff changeset
67 <!--<data format="dot-bracket" name="output_dbn" label="${tool.name} on ${str(input.input_fasta.hid) + ': ' + input.input_fasta.name if $input.method == 'fasta' else $input.input_sequence.upper() }" />-->
0
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
68 </outputs>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
69
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
70 <tests>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
71 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
72 <param name="input_fasta" value="test_01.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
73 <output name="output_dbn" file="test_01.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
74 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
75 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
76 <param name="input_fasta" value="test_02.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
77 <output name="output_dbn" file="test_02.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
78 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
79 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
80 <param name="input_fasta" value="test_03.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
81 <output name="output_dbn" file="test_03.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
82 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
83 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
84 <param name="input_fasta" value="test_04.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
85 <output name="output_dbn" file="test_04.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
86 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
87 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
88 <param name="input_fasta" value="test_05.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
89 <output name="output_dbn" file="test_05.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
90 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
91 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
92 <param name="input_fasta" value="test_06.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
93 <output name="output_dbn" file="test_06.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
94 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
95 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
96 <param name="input_fasta" value="test_07.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
97 <output name="output_dbn" file="test_07.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
98 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
99 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
100 <param name="input_fasta" value="test_08.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
101 <output name="output_dbn" file="test_08.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
102 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
103 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
104 <param name="input_fasta" value="test_09.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
105 <output name="output_dbn" file="test_09.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
106 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
107 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
108 <param name="input_fasta" value="test_10.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
109 <output name="output_dbn" file="test_10.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
110 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
111 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
112 <param name="input_fasta" value="test_11.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
113 <output name="output_dbn" file="test_11.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
114 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
115 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
116 <param name="input_fasta" value="test_12.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
117 <output name="output_dbn" file="test_12.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
118 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
119 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
120 <param name="input_fasta" value="test_13.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
121 <output name="output_dbn" file="test_13.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
122 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
123 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
124 <param name="input_fasta" value="test_14.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
125 <output name="output_dbn" file="test_14.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
126 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
127 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
128 <param name="input_fasta" value="test_15.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
129 <output name="output_dbn" file="test_15.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
130 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
131 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
132 <param name="input_fasta" value="test_16.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
133 <output name="output_dbn" file="test_16.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
134 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
135 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
136 <param name="input_fasta" value="test_17.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
137 <output name="output_dbn" file="test_17.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
138 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
139 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
140 <param name="input_fasta" value="test_18.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
141 <output name="output_dbn" file="test_18.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
142 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
143 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
144 <param name="input_fasta" value="test_19.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
145 <output name="output_dbn" file="test_19.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
146 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
147 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
148 <param name="input_fasta" value="test_20.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
149 <output name="output_dbn" file="test_20.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
150 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
151 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
152 <param name="input_fasta" value="test_21.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
153 <output name="output_dbn" file="test_21.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
154 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
155 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
156 <param name="input_fasta" value="test_22.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
157 <output name="output_dbn" file="test_22.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
158 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
159 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
160 <param name="input_fasta" value="test_23.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
161 <output name="output_dbn" file="test_23.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
162 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
163 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
164 <param name="input_fasta" value="test_24.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
165 <output name="output_dbn" file="test_24.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
166 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
167 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
168 <param name="input_fasta" value="test_25.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
169 <output name="output_dbn" file="test_25.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
170 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
171 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
172 <param name="input_fasta" value="test_26.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
173 <output name="output_dbn" file="test_26.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
174 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
175 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
176 <param name="input_fasta" value="test_27.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
177 <output name="output_dbn" file="test_27.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
178 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
179 <test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
180 <param name="input_fasta" value="test_28.fa" ftype="fasta" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
181 <output name="output_dbn" file="test_28.dbn" />
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
182 </test>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
183 </tests>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
184
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
185 <help><![CDATA[
9
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
186 **What it does**:
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
187
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
188 Segmentation-fold is a application in the field of bioinformatics that
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
189 predicts RNA 2D-structures. The model has an extension with respect to
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
190 the classical Zuker algorithm, to allow new "structure elements" named
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
191 segments and segmentloops. This makes it capable of folding a
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
192 pre-defined substructure with multiple canonical or non-canonical base
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
193 pairs, like K-turns and loop-E-motifs. Some of such sturcture elements
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
194 are present in the corresponding energy table, although custom tables
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
195 can be provided as well.
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
196
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
197
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
198 **Running segmentation-fold**
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
199
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
200 Segmentation-fold has to be provided with a sequence of which it has to
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
201 predict the 2D structure. This can be done using a plain text sequence
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
202 (allowed charset: ACTUG) or a FASTA file. A FASTA file has the following
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
203 syntax:
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
204
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
205 >Sequence name and other details
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
206
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
207 AGUGUAGCUGUGUCGAUCGUAAGUCAG
0
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
208
9
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
209 As the database of free energy parameters will most likely be updated
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
210 over time we have added the possiblity to include this XML file as
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
211 additional parameter. The most up to date version of this file can be
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
212 found at the following url:
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
213
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
214 https://github.com/yhoogstrate/segmentation-fold/blob/master/share/segmentation-fold/segments.xml
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
215
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
216 If you would like to compare the results with a prediction as if the
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
217 segment and segmentloop extension were disabled, you can disable it with
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
218 the given parameter.
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
219
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
220 **Output**
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
221
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
222 The output is in DotBracket format (dbn) and can be visualized with e.g.
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
223 DrawRNAjs or VaRNA.
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
224
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
225 DrawRNAjs can be installed in galaxy by following the instructions at
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
226 the following link:
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
227
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
228 https://github.com/bgruening/galaxytools/tree/master/visualisations/drawrnajs
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
229
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
230 Details on the dbn-format can be found here:
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
231
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
232 https://wiki.galaxyproject.org/Learn/Datatypes#Dbn
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
233
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
234 **Authors**
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
235
8e155ad4151a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
yhoogstrate
parents: 8
diff changeset
236 Youri Hoogstrate (yhoogstrate @ github)
0
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
237 ]]></help>
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
238
11
487f438da099 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c
yhoogstrate
parents: 10
diff changeset
239 <expand macro="citations" />
0
3125baf6e705 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36
yhoogstrate
parents:
diff changeset
240 </tool>