Mercurial > repos > mvdbeek > r_goseq_1_22_0
comparison get_length_and_gc_content.xml @ 0:a6427f7893b0 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
| author | mvdbeek |
|---|---|
| date | Fri, 26 Feb 2016 06:57:47 -0500 |
| parents | |
| children | 0e9424413ab0 |
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| -1:000000000000 | 0:a6427f7893b0 |
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| 1 <tool id="length_and_gc_content" name="gene length and gc content from gtf file" version="0.1.0"> | |
| 2 <description /> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="3.2.1">R</requirement> | |
| 5 <requirement type="package" version="1.22.0">goseq</requirement> | |
| 6 </requirements> | |
| 7 <command interpreter="Rscript"> | |
| 8 get_length_and_gc_content.r --gtf "$gtf" | |
| 9 #if $fastaSource.genomeSource == "indexed": | |
| 10 --fasta "$fastaSource.fasta_pre_installed.fields.path" | |
| 11 #else: | |
| 12 --fasta "$fastaSource.fasta_history" | |
| 13 #end if | |
| 14 --output "$output" | |
| 15 </command> | |
| 16 <inputs> | |
| 17 <param help="The GTF must match the FASTA file" label="GTF file for length and GC calculation" name="gtf" type="data" /> | |
| 18 <conditional name="fastaSource"> | |
| 19 <param help="choose history if you don't see the correct genome fasta" label="Select a reference fasta from your history or use a built-in fasta?" name="genomeSource" type="select"> | |
| 20 <option value="indexed">Use a built-in fasta</option> | |
| 21 <option value="history">Use fasta from history</option> | |
| 22 </param> | |
| 23 <when value="indexed"> | |
| 24 <param help="Select the fasta file from a list of pre-installed genomes" label="Select a fasta sequence" name="fasta_pre_installed" type="select"> | |
| 25 <options from_data_table="all_fasta"/> | |
| 26 </param> | |
| 27 </when> | |
| 28 <when value="history"> | |
| 29 <param format="fasta" label="Select a fasta file, to serve as index reference" name="fasta_history" type="data" /> | |
| 30 </when> | |
| 31 </conditional> | |
| 32 </inputs> | |
| 33 <outputs> | |
| 34 <data format="tabular" label="length and gc content" name="output" /> | |
| 35 </outputs> | |
| 36 <tests></tests> | |
| 37 <help> | |
| 38 | |
| 39 **What it does** | |
| 40 | |
| 41 Returns a tabular file with gene name, length and GC content, based on a supplied GTF and a FASTA file. | |
| 42 | |
| 43 | |
| 44 </help> | |
| 45 <citations> | |
| 46 </citations> | |
| 47 </tool> |