Mercurial > repos > yhoogstrate > segmentation_fold

comparison utils_estimate-energy.xml @ 4:63df1e23f4ff draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 00690c63c51a7f7563f2428c313d7fa75f2657e5-dirty
author yhoogstrate
date Thu, 28 Jul 2016 10:25:37 -0400
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children b7cf9b172cfe
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3:cd1bba1c66b3 4:63df1e23f4ff
1 <tool id="smf_utils_estimate-energy" name="estimate-energy" version="@VERSION@-2">
2 <description>Estimates whether a certain Segment(Loop) is present and for which delta-G this transistion takes place</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <requirements>
9 <requirement type="package" version="2.7.10">python</requirement>
10 <requirement type="package" version="1.9">numpy</requirement>
11 <requirement type="package" version="0.8.2.1">pysam</requirement>
12 <requirement type="package" version="0.6.1">htseq</requirement>
13 <requirement type="package" version="2.0.1">segmentation-fold-utils</requirement>
14
15 <requirement type="package" version="1.6.5">segmentation-fold</requirement>
16 </requirements>
17 <expand macro="stdio" />
18
19 <version_command>echo $(@VERSION_COMMAND_SMF@)", "$(@VERSION_COMMAND_UTILS@)</version_command>
20
21 <command><![CDATA[
22 segmentation-fold-utils
23 estimate-energy
24 -T \${GALAXY_SLOTS:-2}
25 -x
26 #if str($parameters.use_custom_xml) == "true"
27 "${parameters.input_xml}"
28 #else
29 "\$SEGMENTATION_FOLD_DEFAULT_XML"
30 #end if
31
32 -p $precision
33 -r $randomize
34
35 #if $sequences_from_fasta_file:
36 --sequences-from-fasta-file "${sequences_from_fasta_file}"
37 #end if
38
39 $output_list
40 ]]></command>
41
42 <inputs>
43 <conditional name="parameters">
44 <param name="use_custom_xml"
45 type="boolean"
46 truevalue="true"
47 falsevalue="false"
48 selected="false"
49 label="Use segment definition from history" />
50
51 <when value="false" />
52 <when value="true">
53 <param name="input_xml"
54 type="data"
55 format="xml"
56 multiple="false"
57 argument="-x"
58 label="Custom 'segments.xml'-syntaxed file" />
59 </when>
60 </conditional>
61
62 <param name="precision"
63 type="float"
64 value="0.05"
65 min="0"
66 argument="--precision"
67 label="Precision"
68 help="Minimal difference for binary split - the smaller this value the slower. if this value equals 0, the difference is set to infinity (default: 0.05)" />
69
70 <param name="randomize"
71 type="integer"
72 value="0"
73 min="0"
74 argument="--randomize"
75 label="Shuffle each sequence this many times and predict energy of shuffled sequence(s) (default: 0, 0 means disabled)" />
76
77 <param name="sequences_from_fasta_file"
78 type="data"
79 format="fasta"
80 multiple="false"
81 optional="true"
82 argument="--sequences-from-fasta-file"
83 label="Optional sequences to scan for Segment(Loop)s (FASTA)"
84 help="Use sequences from a FASTA file instead of the XML file that contains the segments. In XML files you can explicitly link one Segment(Loop) to one particular sequence instead of doing n*n comparisons (default: None)" />
85 </inputs>
86
87 <outputs>
88 <data format="dbn" name="output_list" label="${tool.name}" />
89 </outputs>
90
91 <tests>
92 <!-- xml * fasta mode -->
93 <test>
94 <param name="use_custom_xml" value="false" ftype="fasta" />
95 <param name="sequences_from_fasta_file" value="SNORD13-revised.fa" ftype="fasta" />
96
97 <output name="output_list" file="SNORD13-revised.scan-for-segments.txt" />
98 </test>
99 <test>
100 <param name="use_custom_xml" value="false" ftype="fasta" />
101 <param name="sequences_from_fasta_file" value="SNORD48-revised.fa" ftype="fasta" />
102
103 <output name="output_list" file="SNORD48-revised.scan-for-segments.txt" />
104 </test>
105 <test>
106 <param name="use_custom_xml" value="false" ftype="fasta" />
107 <param name="sequences_from_fasta_file" value="SNORD114-4-revised.fa" ftype="fasta" />
108
109 <output name="output_list" file="SNORD114-4-revised.scan-for-segments.txt" />
110 </test>
111 <test>
112 <param name="use_custom_xml" value="false" ftype="fasta" />
113 <param name="sequences_from_fasta_file" value="SNORD118-revised.fa" ftype="fasta" />
114
115 <output name="output_list" file="SNORD118-revised.scan-for-segments.txt" />
116 </test>
117
118
119 <!-- xml * xml mode -->
120 <test>
121 <param name="use_custom_xml" value="true" />
122 <param name="input_xml" value="segments_truncated.xml" ftype="xml" />
123 <param name="do_randomization" value="false" />
124 <param name="shuffle_n_times" value="0" />
125
126 <output name="output_list" file="segments_truncated.out.txt" lines_diff="2" />
127 </test>
128 <test>
129 <param name="use_custom_xml" value="true" />
130 <param name="input_xml" value="segments_truncated.xml" ftype="xml" />
131 <param name="do_randomization" value="false" />
132 <param name="shuffle_n_times" value="1" />
133
134 <output name="output_list" file="segments_truncated.2.out.txt" lines_diff="10" />
135 </test>
136 </tests>
137
138 <help><![CDATA[
139 This is an utility of the segmentation-fold package that allows to scan for the presence of certain segments.
140 If present, it will also scan for the Gibbs free energy necessairy the segment has to provide to contribute to the optimal structure.
141 ]]></help>
142
143 <expand macro="citations" />
144 </tool>