Mercurial > repos > mvdbeek > r_goseq_1_22_0
comparison get_length_and_gc_content.xml @ 15:e3b1dd2f7f70 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
author | mvdbeek |
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date | Thu, 25 Feb 2016 07:24:31 -0500 |
parents | ade115e181d7 |
children | 1b03f6232900 |
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14:ade115e181d7 | 15:e3b1dd2f7f70 |
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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_pre_installed.fields.path" | 10 --fasta "$fastaSource.fasta_pre_installed.fields.path" |
11 #else: | 11 #else: |
12 --fasta "$fastaSource.history.fasta_history" | 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" /> |
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"> | 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_history" label="Select a fasta file, to serve as index reference" name="fasta" type="data" /> | 29 <param format="fasta" label="Select a fasta file, to serve as index reference" name="fasta_history" 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" /> |