Mercurial > repos > yhoogstrate > segmentation_fold

annotate utils_find-boxes.xml @ 16:7e5b96d45f8d draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit c6608bd5256e5c54cb2e01be6c184da0d2b08a7c-dirty
author yhoogstrate
date Thu, 19 May 2016 05:41:48 -0400
parents 5de95e0173a7
children 3fbde4864e00
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1 <tool id="smf_utils_find-boxes" name="find-boxes" version="@VERSION@-0">
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2 <description>Finds all occurances of two given boxes (sequence motifs) within a FASTA file</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <requirements>
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9 <requirement type="package" version="2.7.10">python</requirement>
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10 <requirement type="package" version="1.9">numpy</requirement>
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11 <requirement type="package" version="0.8.2.1">pysam</requirement>
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12 <requirement type="package" version="2.0.0">segmentation-fold-utils</requirement>
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13 </requirements>
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14
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15 <expand macro="stdio" />
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17 <version_command>@VERSION_COMMAND_UTILS@</version_command>
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19 <command><![CDATA[
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20 segmentation-fold-utils
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21 find-boxes
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22 --box1 '${box1}'
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23 --box2 '${box2}'
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24 $forward
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25 $reverse
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26 '${fasta_input}'
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27 '${bed_output}'
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28 ]]></command>
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30 <inputs>
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31 <param name="fasta_input"
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32 type="data"
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33 format="fasta"
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34 argument="-f"
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35 label="Fasta file with RNA-sequece" />
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36
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37 <param name="box1"
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38 type="text"
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39 value="NRUGAUG"
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40 argument="--box1"
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41 label="Sequence of box1 (default = C-box: 'NRUGAUG')"
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42 help="Sequence encoding can be found at the following url: https://en.wikipedia.org/wiki/FASTA_format#Sequence_representations" />
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43
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44 <param name="box2"
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45 type="text"
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46 value="CUGA"
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47 argument="--box2"
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48 label="Sequence of box2 (default = D-box: 'CUGA')"
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49 help="Sequence encoding can be found at the following url: https://en.wikipedia.org/wiki/FASTA_format#Sequence_representations" />
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50
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51 <param name="forward"
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52 type="boolean"
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53 truevalue="--forward"
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54 falsevalue="--no-forward"
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55 checked="true"
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56 label="Search in the forward direction of the reference sequence" />
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57
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58 <param name="reverse"
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59 type="boolean"
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60 truevalue="--reverse"
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61 falsevalue="--no-reverse"
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62 checked="true"
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63 label="Search in the reverse complement of the reference sequence" />
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64 </inputs>
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65
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66 <outputs>
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67 <data format="bed"
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68 name="bed_output"
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69 label="${tool.name} on ${str($fasta_input.hid) + ': ' + $fasta_input.name}" />
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70 </outputs>
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71
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72 <tests>
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73 <test>
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74 <param name="fasta_input" value="FindBoxes.genome.fa" format="fasta" />
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75 <param name="box1" value="NRUGAUG" />
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76 <param name="box2" value="CUGA" />
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77 <param name="forward" value="--forward" />
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78 <param name="reverse" value="--reverse" />
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79
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80 <output name="bed_output" file="FindBoxes.test_02.bed" />
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81 </test>
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82 </tests>
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83
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84 <help><![CDATA[
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85 Scans a FASTA reference for BOX motifs (like C- and D-box) and reports them in a BED file
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86 ]]></help>
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87
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88 <expand macro="citations" />
487f438da099 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c
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89 </tool>