Mercurial > repos > 19zhang > iwa_mirna

comparison genomeRetrival.xml @ 1:34b51ff7d639 draft default tip

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author 19zhang
date Tue, 13 Oct 2020 07:08:31 +0000
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0:aa09089f2c31 1:34b51ff7d639
1 <tool id="genomeindex" name="genomePrepare" workflow_compatible="false" version="20.05">
2 <!-- <description>get genome sequences, annotation and file path (built-in or uploaded)</description> -->
3
4 <command><![CDATA[
5 bash ${__tool_directory__}/scripts/obtainSpecies.sh
6 --curpath ${__tool_directory__}
7 #if $genometype.datainput == "UploadData":
8 --name "$genometype.speciename"
9 --genome $genometype.genomeData
10 --gff $genometype.annotationData
11 --otherrna $genometype.otherrna
12 --transcript $genometype.transcriptsData
13 --protein $genometype.proteinsData
14 --speciesout $filePath
15 --infout $infout1
16 #else
17 --ensembl "$genometype.buildplant"
18 --verorder "$genometype.version"
19
20 --outgenome $outgenome
21 --outgff3 $outgff3
22 --outtranscript $outtranscript
23 --outtrsnsnoRNA $outtrsnsnoRNA
24 --outprotein $outprotein
25
26 --speciesout $builtinPath
27 --infout $infout2
28 #end if
29
30 ]]></command>
31
32 <inputs>
33 <conditional name="genometype">
34 <!-- <param name="datainput" type="boolean" truevalue="yes" falsevalue="no" checked="true"
35 label="Upload your own genome data?" help ="User can also select built-in species by clicking the button-No " /> -->
36 <param type="select" name="datainput" display="radio" multiple="false" help="Note: for 'upload from local disk', please upload files by uploadFile function first."
37 label="Two ways for preparing genome data:" >
38 <option value="BuiltinSpecies" selected="true" > Download from EnsemblPlants database</option>
39 <option value="UploadData"> Upload from local disk</option>
40 </param>
41
42 <when value="BuiltinSpecies">
43 <param name="buildplant" type="select"
44 label="Species (support for 61 species)"
45 help="">
46 <options from_data_table="ensembl_plant" >
47 <!-- <filter type="sort_by" column="1"/>
48 <validator type="no_options" message="No indexes are available for the selected input dataset"/> -->
49 </options>
50 </param>
51
52 <param name="version" type="select"
53 label="Database version"
54 help="">
55 <options from_data_table="ensembl_plant_version">
56 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
57 </options>
58 </param>
59
60 </when>
61
62 <when value="UploadData">
63 <param type="text" name="speciename" value=""
64 label="Species"
65 help="e.g. Arabidopsis thaliana" />
66
67 <param name="genomeData" type="data" format="fasta" optional="true" label="Genome sequences (.fasta)" />
68 <param name="annotationData" type="data" format="gff3" optional="true" label="Annotation file (.gff3)" />
69 <param name="otherrna" type="data" format="fasta" optional="true" label="t/r/sn/snoRNA sequences (.fasta)" />
70 <param name="transcriptsData" type="data" format="fasta" optional="true" label="cDNA sequences (.fasta)" />
71 <param name="proteinsData" type="data" format="fasta" optional="true" label="Optional: Protein sequences (.fasta)" />
72 </when>
73 </conditional>
74 </inputs>
75
76 <stdio><exit_code range="1:" level="fatal" description="Error when running ${tool.name}"/></stdio>
77
78 <outputs>
79 <data format="simple" name="filePath" label="${genometype.speciename.value}">
80 <filter> genometype['datainput'] == "UploadData" </filter>
81 </data>
82 <data format="pdf" name="infout1" label="${genometype.speciename.value} | ${tool.name} | Summary of genomic features">
83 <filter> genometype['datainput'] == "UploadData" </filter>
84 </data>
85 <data format="simple" name="builtinPath" label="${genometype.buildplant.value}_${genometype.version.value}">
86 <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
87 </data>
88 <data format="pdf" name="infout2" label="${genometype.buildplant.value}_${genometype.version.value} | ${tool.name} | Summary of genomic features">
89 <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
90 </data>
91 <data format="gz" name="outgenome" label="${genometype.buildplant.value}_${genometype.version.value} | ${tool.name} | Genome sequences ">
92 <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
93 </data>
94 <data format="fasta" name="outtrsnsnoRNA" label="${genometype.buildplant.value}_${genometype.version.value} | ${tool.name} | t/r/sn/snoRNA sequences">
95 <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
96 </data>
97 <data format="gff3" name="outgff3" label="${genometype.buildplant.value}_${genometype.version.value} | ${tool.name} | GFF3 annotations">
98 <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
99 </data>
100 <data format="fasta" name="outtranscript" label="${genometype.buildplant.value}_${genometype.version.value} | ${tool.name} | cDNA sequences">
101 <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
102 </data>
103 <data format="fasta" name="outprotein" label="${genometype.buildplant.value}_${genometype.version.value} | ${tool.name} | Protein sequences">
104 <filter> genometype['datainput'] == "BuiltinSpecies" </filter>
105 </data>
106
107 </outputs>
108
109 <tests>
110 <test>
111 <param name="genomeData" value="Arabidopsis_genome.fa" ftype="fasta" />
112 <param name="annotationData" value="Arabidopsis_annotation.gff3" ftype="fasta" />
113 <output name="filePath" file="genomePrepare: References_of_Arabidopsis_thaliana.simple" ftype="simple" />
114 </test>
115
116 </tests>
117
118
119 <help><![CDATA[
120
121 .. class:: donemark
122
123 **What it does**
124
125 This tool provides two ways for preparing genome data:
126
127 1. Automatically download genomes, annotations, t/r/sn/snoRNAs (i.e. tRNAs, rRNAs, snRNAs, and snoRNAs), cDNAs, and proteins from `EnsemblPlants database`_.
128 2. Upload genomic data for species not included in EnsemblPlants.
129
130 .. class:: infomark
131
132 **Outputs**
133
134 - A file containing the path of formatted genome sequences and annotations. Index files of the reference genome and t/r/sn/snoRNA sequences in this path are used for 'miRNAPredict' analysis.
135 - Summary of the number and length of genomic features.
136 - Genome sequences, annotation file in GFF3 format, t/r/sn/snoRNA sequences, cDNAs, and protein sequences.
137
138 .. _`EnsemblPlants database`: ftp://ftp.ensemblgenomes.org/pub/plants
139
140 |
141
142 ]]></help>
143
144 <citations>
145 <citation type="doi">10.1007/978-1-4939-6658-5_1</citation>
146 </citations>
147
148 </tool>