comparison armdb.xml @ 2:97d83ccbba75 draft

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author glogobyte
date Wed, 13 Oct 2021 16:23:23 +0000
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1:d133caf020a7 2:97d83ccbba75
1 <tool id="ArmDB" name="ArmDB: Generation of Pre-miRNA arm reference DB (5p and 3p arms)" version="0.1.0">
2 <requirements>
3 <requirement type="package" version="2.28.0">Bedtools</requirement>
4 <requirement type="package" version="3.7.4">python</requirement>
5 </requirements>
6 <command>
7 #if $mir_input.analysis == "1":
8 #set path=$mir_input.genome1.fields.dbkey
9 python $__tool_directory__/armdb_mirbase.py -pos $positions -tool_dir $__tool_directory__ -gff3 "$path" -gen $mir_input.genome1.fields.value
10 #end if
11 #if $mir_input.analysis == "2":
12 #set path=$mir_input.genome2.fields.value
13 python $__tool_directory__/armdb_mirgene.py -pos $positions -tool_dir $__tool_directory__ -sym "$path"
14 #end if
15 </command>
16 <inputs>
17 <conditional name="mir_input">
18 <param name="analysis" type="select" label="Choose reference Mir database" help="Choose which database prefer to be used.">
19 <option value="1" selected="true">MirBase</option>
20 <option value="2">MirGene</option>
21 </param>
22 <when value="1">
23 <param name="genome1" type="select" label="Choose organism" help="If your genome coordinates of interest is not listed, contact the Galaxy team">
24 <options from_data_table="mirbase" />
25 </param>
26 </when>
27 <when value="2">
28 <param name="genome2" type="select" label="Choose organism" help="If your genome coordinates of interest is not listed, contact the" >
29 <options from_data_table="mirgene" />
30 </param>
31 </when>
32 </conditional>
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" />
34 </inputs>
35 <outputs>
36 <data name="shifted_gff1" format="txt" label="Custom Bed file" from_work_dir="$__tool_directory__/shifted_mirnas.bed">
37 <filter>mir_input['analysis']== "1" </filter>
38 </data>
39 <data name="normal_gff1" format="fasta" label="Official Bed file" from_work_dir="$__tool_directory__/original_mirnas.bed" >
40 <filter>mir_input['analysis']== "1" </filter>
41 </data>
42 <data name="custom reference genome1" format="fasta" label="Custom reference arms" from_work_dir="$__tool_directory__/new_ref.fa" >
43 <filter>mir_input['analysis']== "1" </filter>
44 </data>
45
46 <data name="shifted_gff" format="txt" label="Mature and star miRNA sequences" from_work_dir="$__tool_directory__/shifted_mirnas.bed">
47 <filter>mir_input['analysis']== "2" </filter>
48 </data>
49 <data name="normal_gff" format="fasta" label="Primary transcripts with flanks" from_work_dir="$__tool_directory__/original_mirnas.bed" >
50 <filter>mir_input['analysis']== "2" </filter>
51 </data>
52 <data name="custom reference genome" format="fasta" label="Custom reference arms" from_work_dir="$__tool_directory__/new_ref.fa" >
53 <filter>mir_input['analysis']== "2" </filter>
54 </data>
55
56 </outputs>
57 <help>
58
59 </help>
60 </tool>