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comparison utils_find-boxes.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_find-boxes" name="find-boxes" version="@VERSION@-1">
2 <description>Finds all occurances of two given boxes (sequence motifs) within a FASTA file</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 </requirements>
15
16 <expand macro="stdio" />
17
18 <version_command>@VERSION_COMMAND_UTILS@</version_command>
19
20 <command><![CDATA[
21 segmentation-fold-utils
22 find-boxes
23 --box1 '${box1}'
24 --box2 '${box2}'
25 $forward
26 $reverse
27 '${fasta_input}'
28 '${bed_output}'
29 ]]></command>
30
31 <inputs>
32 <param name="fasta_input"
33 type="data"
34 format="fasta"
35 argument="-f"
36 label="Fasta file with RNA-sequece" />
37
38 <param name="box1"
39 type="text"
40 value="NRUGAUG"
41 argument="--box1"
42 label="Sequence of box1 (default = C-box: 'NRUGAUG')"
43 help="Sequence encoding can be found at the following url: https://en.wikipedia.org/wiki/FASTA_format#Sequence_representations" />
44
45 <param name="box2"
46 type="text"
47 value="CUGA"
48 argument="--box2"
49 label="Sequence of box2 (default = D-box: 'CUGA')"
50 help="Sequence encoding can be found at the following url: https://en.wikipedia.org/wiki/FASTA_format#Sequence_representations" />
51
52 <param name="forward"
53 type="boolean"
54 truevalue="--forward"
55 falsevalue="--no-forward"
56 checked="true"
57 label="Search in the forward direction of the reference sequence" />
58
59 <param name="reverse"
60 type="boolean"
61 truevalue="--reverse"
62 falsevalue="--no-reverse"
63 checked="true"
64 label="Search in the reverse complement of the reference sequence" />
65 </inputs>
66
67 <outputs>
68 <data format="bed"
69 name="bed_output"
70 label="${tool.name} on ${str($fasta_input.hid) + ': ' + $fasta_input.name}" />
71 </outputs>
72
73 <tests>
74 <test>
75 <param name="fasta_input" value="FindBoxes.genome.fa" format="fasta" />
76 <param name="box1" value="NRUGAUG" />
77 <param name="box2" value="CUGA" />
78 <param name="forward" value="--forward" />
79 <param name="reverse" value="--reverse" />
80
81 <output name="bed_output" file="FindBoxes.test_02.bed" />
82 </test>
83 </tests>
84
85 <help><![CDATA[
86 Scans a FASTA reference for BOX motifs (like C- and D-box) and reports them in a BED file
87 ]]></help>
88
89 <expand macro="citations" />
90 </tool>