Mercurial > repos > mvdbeek > r_goseq_1_22_0

comparison get_length_and_gc_content.xml @ 15:e3b1dd2f7f70 draft

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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 07:24:31 -0500
parents ade115e181d7
children 1b03f6232900
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14:ade115e181d7 15:e3b1dd2f7f70
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" />