Mercurial > repos > earlhaminst > gstf_preparation

comparison gstf_preparation.xml @ 6:56bbdbfe3eaa draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit fa875eea77a9471acada2b7b8882a0467994c960
author earlhaminst
date Wed, 25 Apr 2018 11:00:33 -0400
parents 284f64ad9d43
children 9ef7661e8e9c
comparison
equal deleted inserted replaced
5:b3ba0c84667c 6:56bbdbfe3eaa
18 --headers 18 --headers
19 #end if 19 #end if
20 #if $longestCDS 20 #if $longestCDS
21 -l 21 -l
22 #end if 22 #end if
23 #if $regions
24 --regions '$regions'
25 #end if
23 -o '$output_db' 26 -o '$output_db'
24 --of '$output_fasta' 27 --of '$output_fasta'
28 --ff '$filtered_fasta'
25 ]]> 29 ]]>
26 </command> 30 </command>
27 31
28 <inputs> 32 <inputs>
29 <repeat name="queries" title="GFF3 dataset"> 33 <repeat name="queries" title="GFF3 dataset">
34 </repeat> 38 </repeat>
35 <param name="json" type="data" format="json" multiple="true" optional="true" label="Gene features in JSON format generated by 'Get features by Ensembl ID' tool" /> 39 <param name="json" type="data" format="json" multiple="true" optional="true" label="Gene features in JSON format generated by 'Get features by Ensembl ID' tool" />
36 <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding FASTA datasets" help="Each FASTA header line should start with a transcript id" /> 40 <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding FASTA datasets" help="Each FASTA header line should start with a transcript id" />
37 <param name="longestCDS" type="boolean" checked="false" label="Keep only the longest CDS per gene" /> 41 <param name="longestCDS" type="boolean" checked="false" label="Keep only the longest CDS per gene" />
38 <param name="headers" type="boolean" checked="true" label="Change the header line of the FASTA sequences to the &gt;TranscriptId_species format" help="As required by TreeBest, part of the GeneSeqToFamily workflow" /> 42 <param name="headers" type="boolean" checked="true" label="Change the header line of the FASTA sequences to the &gt;TranscriptId_species format" help="As required by TreeBest, part of the GeneSeqToFamily workflow" />
43 <param name="regions" type="text" optional="true" label="Comma-separated list of region IDs (e.g. chromosomes or scaffolds) for which FASTA sequences should be filtered" help="Region IDs are in the `seqid` column for GFF3 and in the `seq_region_name` field in JSON. This is typically used to filter chromosomes with a non-standard genetic code, like mitochondria, to be analysed separately" />
39 </inputs> 44 </inputs>
40 45
41 <outputs> 46 <outputs>
42 <data name="output_db" format="sqlite" label="${tool.name} on ${on_string}: SQLite" /> 47 <data name="output_db" format="sqlite" label="${tool.name} on ${on_string}: SQLite" />
43 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: FASTA" /> 48 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: FASTA" />
49 <data name="filtered_fasta" format="fasta" label="${tool.name} on ${on_string}: filtered sequences" />
44 </outputs> 50 </outputs>
45 51
46 <tests> 52 <tests>
47 <test> 53 <test>
48 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" /> 54 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
51 <param name="longestCDS" value="false" /> 57 <param name="longestCDS" value="false" />
52 <param name="headers" value="true" /> 58 <param name="headers" value="true" />
53 59
54 <output name="output_db" file="test1.sqlite" compare="sim_size" /> 60 <output name="output_db" file="test1.sqlite" compare="sim_size" />
55 <output name="output_fasta" file="test1.fasta" /> 61 <output name="output_fasta" file="test1.fasta" />
62 <output name="filtered_fasta" file="test1.ns.fasta" />
56 </test> 63 </test>
57 <test> 64 <test>
58 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" /> 65 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
59 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" /> 66 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
60 <param name="genome" value="caenorhabditis_elegans" /> 67 <param name="genome" value="caenorhabditis_elegans" />
61 <param name="longestCDS" value="true" /> 68 <param name="longestCDS" value="true" />
62 <param name="headers" value="true" /> 69 <param name="headers" value="true" />
63 70
64 <output name="output_db" file="test1.sqlite" compare="sim_size" /> 71 <output name="output_db" file="test1.sqlite" compare="sim_size" />
65 <output name="output_fasta" file="test1_longest.fasta" /> 72 <output name="output_fasta" file="test1_longest.fasta" />
73 <output name="filtered_fasta" file="test1.ns.fasta" />
66 </test> 74 </test>
67 <test> 75 <test>
68 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" /> 76 <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
69 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" /> 77 <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
70 <param name="genome" value="caenorhabditis_elegans" /> 78 <param name="genome" value="caenorhabditis_elegans" />
71 <param name="longestCDS" value="false" /> 79 <param name="longestCDS" value="false" />
72 <param name="headers" value="false" /> 80 <param name="headers" value="false" />
73 81
74 <output name="output_db" file="test1.sqlite" compare="sim_size" /> 82 <output name="output_db" file="test1.sqlite" compare="sim_size" />
75 <output name="output_fasta" file="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" /> 83 <output name="output_fasta" file="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
84 <output name="filtered_fasta" file="test1.ns.fasta" />
76 </test> 85 </test>
77 <test> 86 <test>
78 <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" /> 87 <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
79 <param name="json" ftype="json" value="gene.json" /> 88 <param name="json" ftype="json" value="gene.json" />
80 <param name="longestCDS" value="false" /> 89 <param name="longestCDS" value="false" />
81 <param name="headers" value="true" /> 90 <param name="headers" value="true" />
82 91
83 <output name="output_db" file="test2.sqlite" compare="sim_size" /> 92 <output name="output_db" file="test4.sqlite" compare="sim_size" />
84 <output name="output_fasta" file="test2.fasta" /> 93 <output name="output_fasta" file="test4.fasta" />
94 <output name="filtered_fasta" file="test4.ns.fasta" />
95 </test>
96 <test>
97 <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
98 <param name="json" ftype="json" value="gene.json" />
99 <param name="longestCDS" value="false" />
100 <param name="headers" value="true" />
101 <param name="regions" value="X" />
102
103 <output name="output_db" file="test5.sqlite" compare="sim_size" />
104 <output name="output_fasta" file="test5_filtered.fasta" />
105 <output name="filtered_fasta" file="test5.ns.fasta" />
85 </test> 106 </test>
86 </tests> 107 </tests>
87 <help> 108 <help>
88 <![CDATA[ 109 <![CDATA[
89 **What it does** 110 **What it does**