Mercurial > repos > mvdbeek > r_goseq_1_22_0
comparison get_length_and_gc_content.xml @ 9:d1eed994287a draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
| author | mvdbeek |
|---|---|
| date | Thu, 25 Feb 2016 06:16:23 -0500 |
| parents | f036e2d66c85 |
| children | 1802ccf465b8 |
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| 8:f036e2d66c85 | 9:d1eed994287a |
|---|---|
| 5 <requirement type="package" version="1.22.0">goseq</requirement> | 5 <requirement type="package" version="1.22.0">goseq</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <command interpreter="Rscript"> | 7 <command interpreter="Rscript"> |
| 8 get_length_and_gc_content.r --gtf "$gtf" | 8 get_length_and_gc_content.r --gtf "$gtf" |
| 9 #if $fastaSource.genomeSource == "indexed": | 9 #if $fastaSource.genomeSource == "indexed": |
| 10 --fasta "$fastaSource.fasta.fields.path" | 10 --fasta "$fastaSource.fasta_pre_installed.fields.path" |
| 11 #else: | 11 #else: |
| 12 --fasta "$fastaSource.fasta" | 12 --fasta "$fastaSource.fasta_history" |
| 13 #end if | 13 #end if |
| 14 --output "output" | 14 --output "output" |
| 15 </command> | 15 </command> |
| 16 <inputs> | 16 <inputs> |
| 17 <param help="The GTF must match the FASTA file" label="GTF file for length and GC calculation" name="gtf" type="data" /> | 17 <param help="The GTF must match the FASTA file" label="GTF file for length and GC calculation" name="gtf" type="data" /> |
| 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"> | 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> | 20 <option value="indexed">Use a built-in fasta</option> |
| 21 <option value="history">Use fasta from history</option> | 21 <option value="history">Use fasta from history</option> |
| 22 </param> | 22 </param> |
| 23 <when value="indexed"> | 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" type="select"> | 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"/> | 25 <options from_data_table="all_fasta"/> |
| 26 </param> | 26 </param> |
| 27 </when> | 27 </when> |
| 28 <when value="history"> | 28 <when value="history"> |
| 29 <param format="fasta" label="Select a fasta file, to serve as index reference" name="fasta" type="data" /> | 29 <param format="fasta_history" label="Select a fasta file, to serve as index reference" name="fasta" type="data" /> |
| 30 </when> | 30 </when> |
| 31 </conditional> | 31 </conditional> |
| 32 </inputs> | 32 </inputs> |
| 33 <outputs> | 33 <outputs> |
| 34 <data format="tabular" label="length and gc content" name="output" /> | 34 <data format="tabular" label="length and gc content" name="output" /> |