Mercurial > repos > yhoogstrate > segmentation_fold

annotate utils_find-boxes.xml @ 26:660c25c66c8a draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/segmentation_fold commit 3a3c1d069e0a079d8ea7c0b4ac856ef24141b1aa
author erasmus-medical-center
date Fri, 24 Feb 2017 04:18:08 -0500
parents 44330a54b8eb
children
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3fbde4864e00 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 3814f709ce964e99fe3cf2f979c11f8f3b87bce3-dirty
yhoogstrate
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1 <tool id="smf_utils_find-boxes" name="find-boxes" version="@VERSION@-1">
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2 <description>Finds all occurances of two given boxes (sequence motifs) within a FASTA file</description>
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3
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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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7
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660c25c66c8a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/segmentation_fold commit 3a3c1d069e0a079d8ea7c0b4ac856ef24141b1aa
erasmus-medical-center
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8 <expand macro="requirements" />
660c25c66c8a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/segmentation_fold commit 3a3c1d069e0a079d8ea7c0b4ac856ef24141b1aa
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9 <expand macro="version_command" />
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11 <command detect_errors="aggressive"><![CDATA[
11
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12 segmentation-fold-utils
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13 find-boxes
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14 --box1 '${box1}'
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15 --box2 '${box2}'
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16 $forward
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17 $reverse
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18 '${fasta_input}'
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19 '${bed_output}'
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20 ]]></command>
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22 <inputs>
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23 <param name="fasta_input"
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24 type="data"
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25 format="fasta"
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26 argument="-f"
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27 label="Fasta file with RNA-sequece" />
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29 <param name="box1"
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30 type="text"
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31 value="NRUGAUG"
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32 argument="--box1"
487f438da099 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c
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33 label="Sequence of box1 (default = C-box: 'NRUGAUG')"
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34 help="Sequence encoding can be found at the following url: https://en.wikipedia.org/wiki/FASTA_format#Sequence_representations" />
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35
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36 <param name="box2"
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37 type="text"
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38 value="CUGA"
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39 argument="--box2"
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40 label="Sequence of box2 (default = D-box: 'CUGA')"
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41 help="Sequence encoding can be found at the following url: https://en.wikipedia.org/wiki/FASTA_format#Sequence_representations" />
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42
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43 <param name="forward"
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44 type="boolean"
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45 truevalue="--forward"
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46 falsevalue="--no-forward"
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47 checked="true"
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48 label="Search in the forward direction of the reference sequence" />
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49
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50 <param name="reverse"
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51 type="boolean"
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52 truevalue="--reverse"
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53 falsevalue="--no-reverse"
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54 checked="true"
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55 label="Search in the reverse complement of the reference sequence" />
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56 </inputs>
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57
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58 <outputs>
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59 <data format="bed"
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60 name="bed_output"
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61 label="${tool.name} on ${str($fasta_input.hid) + ': ' + $fasta_input.name}" />
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62 </outputs>
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63
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64 <tests>
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65 <test>
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66 <param name="fasta_input" value="FindBoxes.genome.fa" ftype="fasta" />
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67 <param name="box1" value="NRUGAUG" />
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68 <param name="box2" value="CUGA" />
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69 <param name="forward" value="--forward" />
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70 <param name="reverse" value="--reverse" />
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71
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72 <output name="bed_output" file="FindBoxes.test_02.bed" />
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73 </test>
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74 </tests>
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75
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76 <help><![CDATA[
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77 Scans a FASTA reference for BOX motifs (like C- and D-box) and reports them in a BED file
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78 ]]></help>
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79
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80 <expand macro="citations" />
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81 </tool>