Mercurial > repos > mvdbeek > r_goseq_1_22_0

comparison get_length_and_gc_content.xml @ 6:0e9424413ab0 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
author mvdbeek
date Thu, 03 Mar 2016 09:56:51 -0500
parents a6427f7893b0
children
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5:b79c65c90744 6:0e9424413ab0
1 <tool id="length_and_gc_content" name="gene length and gc content from gtf file" version="0.1.0"> 1 <tool id="length_and_gc_content" name="gene length and gc content" version="0.1.0">
2 <description /> 2 <description>from GTF file</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="3.2.1">R</requirement> 4 <import>go_macros.xml</import>
5 <requirement type="package" version="1.22.0">goseq</requirement> 5 </macros>
6 </requirements> 6 <expand macro="requirements" />
7 <expand macro="stdio" />
7 <command interpreter="Rscript"> 8 <command interpreter="Rscript">
8 get_length_and_gc_content.r --gtf "$gtf" 9 get_length_and_gc_content.r --gtf "$gtf"
9 #if $fastaSource.genomeSource == "indexed": 10 #if $fastaSource.genomeSource == "indexed":
10 --fasta "$fastaSource.fasta_pre_installed.fields.path" 11 --fasta "$fastaSource.fasta_pre_installed.fields.path"
11 #else: 12 #else:
12 --fasta "$fastaSource.fasta_history" 13 --fasta "$fastaSource.fasta_history"
13 #end if 14 #end if
14 --output "$output" 15 --length "$length"
16 --gc_content "$gc_content"
15 </command> 17 </command>
16 <inputs> 18 <inputs>
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="The GTF must match the FASTA file" label="GTF file for length and GC calculation" name="gtf" type="data" format="gtf" />
18 <conditional name="fastaSource"> 20 <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"> 21 <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> 22 <option value="indexed">Use a built-in fasta</option>
21 <option value="history">Use fasta from history</option> 23 <option value="history">Use fasta from history</option>
22 </param> 24 </param>
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"> 26 <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"/> 27 <options from_data_table="all_fasta"/>
26 </param> 28 </param>
27 </when> 29 </when>
28 <when value="history"> 30 <when value="history">
29 <param format="fasta" label="Select a fasta file, to serve as index reference" name="fasta_history" type="data" /> 31 <param format="fasta" label="Select a fasta file that matches the supplied GTF file" name="fasta_history" type="data" />
30 </when> 32 </when>
31 </conditional> 33 </conditional>
32 </inputs> 34 </inputs>
33 <outputs> 35 <outputs>
34 <data format="tabular" label="length and gc content" name="output" /> 36 <data format="tabular" label="gene length" name="length">
37 <!-- future: set this when 16.04 has been released
38 <actions>
39 <action name="column_names" type="metadata" default="gene,length" />
40 </actions>
41 -->
42 </data>
43 <data format="tabular" label="gene gc content" name="gc_content">
44 <!-- future: set this when 16.04 has been released
45 <actions>
46 <action name="column_names" type="metadata" default="gene,gc_content" />
47 </actions>
48 -->
49 </data>
35 </outputs> 50 </outputs>
36 <tests></tests> 51 <tests>
52 <test>
53 <param name="gtf" value="in.gtf" ftype="gtf"></param>
54 <param name="fastaSource|genomeSource" value="history"></param>
55 <param name="fastaSource|fasta_history" value="in.fasta" ftype="fasta"></param>
56 <output name="length" file="length.tab"></output>
57 <output name="gc_content" file="gc.tab"></output>
58 </test>
59 </tests>
37 <help> 60 <help>
38 61
39 **What it does** 62 **What it does**
40 63
41 Returns a tabular file with gene name, length and GC content, based on a supplied GTF and a FASTA file. 64 Returns a tabular file with gene id and length and a tabular file with gene id and GC content, based on a supplied GTF and a FASTA file.
42 65
43 66
44 </help> 67 </help>
45 <citations> 68 <citations>
46 </citations> 69 </citations>