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1 <tool id="ArmDB" name="ArmDB: Generation of Pre-miRNA arm reference DB (5p and 3p arms)" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="2.28.0">Bedtools</requirement>
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4 <requirement type="package" version="3.7.4">python</requirement>
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5 </requirements>
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6 <command>
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7 #if $mir_input.analysis == "1":
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8 #set path=$mir_input.genome1.fields.dbkey
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9 python $__tool_directory__/pre_mirbase.py -pos $positions -tool_dir $__tool_directory__ -gff3 "$path" -gen $mir_input.genome1.fields.value
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10 #end if
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11 #if $mir_input.analysis == "2":
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12 #set path=$mir_input.genome2.fields.value
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13 python $__tool_directory__/pre_mirgene.py -pos $positions -tool_dir $__tool_directory__ -sym "$path"
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14 #end if
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15 </command>
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16 <inputs>
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17 <conditional name="mir_input">
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18 <param name="analysis" type="select" label="Choose reference Mir database" help="Choose which database prefer to be used.">
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19 <option value="1" selected="true">MirBase</option>
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20 <option value="2">MirGene</option>
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21 </param>
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22 <when value="1">
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23 <param name="genome1" type="select" label="Choose organism" help="If your genome coordinates of interest is not listed, contact the Galaxy team">
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24 <options from_data_table="mirbase" />
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25 </param>
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26 </when>
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27 <when value="2">
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28 <param name="genome2" type="select" label="Choose organism" help="If your genome coordinates of interest is not listed, contact the" >
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29 <options from_data_table="mirgene" />
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30 </param>
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31 </when>
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32 </conditional>
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33 <param name="positions" type="integer" min="0" max="8" value="1" label="Custom Arm length" help="Choose how many nucleotides you want to extend the 5p and 3p mature sequences to create the refernce arms" />
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34 </inputs>
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35 <outputs>
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36 <data name="shifted_gff1" format="txt" label="Custom Bed file" from_work_dir="$__tool_directory__/shifted_mirnas.bed">
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37 <filter>mir_input['analysis']== "1" </filter>
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38 </data>
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39 <data name="normal_gff1" format="fasta" label="Official Bed file" from_work_dir="$__tool_directory__/original_mirnas.bed" >
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40 <filter>mir_input['analysis']== "1" </filter>
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41 </data>
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42 <data name="custom reference genome1" format="fasta" label="Custom reference arms" from_work_dir="$__tool_directory__/new_ref.fa" >
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43 <filter>mir_input['analysis']== "1" </filter>
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44 </data>
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45
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46 <data name="shifted_gff" format="txt" label="Mature and star miRNA sequences" from_work_dir="$__tool_directory__/shifted_mirnas.bed">
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47 <filter>mir_input['analysis']== "2" </filter>
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48 </data>
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49 <data name="normal_gff" format="fasta" label="Primary transcripts with flanks" from_work_dir="$__tool_directory__/original_mirnas.bed" >
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50 <filter>mir_input['analysis']== "2" </filter>
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51 </data>
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52 <data name="custom reference genome" format="fasta" label="Custom reference arms" from_work_dir="$__tool_directory__/new_ref.fa" >
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53 <filter>mir_input['analysis']== "2" </filter>
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54 </data>
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55
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56 </outputs>
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57 <help><![CDATA[
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58 .. class:: infomark
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59
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60 **What it does**
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61
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62 -----
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63
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64 **Inputs**
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65
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66 - Genome coordinates in General Feature Format (GFF3) or FASTA files of RefSeq miRNAs
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67
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68 ArmDB takes genome coordinates (GFF3) files from MirBase or FASTA files from MirGene as input. GFF3 files and FASTA files are downloaded directly from the databases.
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69
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70 .. image:: armdb.png
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71
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72 **Outputs**
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73
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74 - ArmDB generates FASTA files containing the custom reference arms that are produced with the user-defined nucleotides extension of the RefSeq sequences (up to 8 nt)
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75
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76 ]]></help>
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77 <citations>
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78 <citation type="doi">10.3390/cancers13225663</citation>
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79 </citations>
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80 </tool>
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