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comparison rsem_prepare_reference.xml @ 3:59459de65740

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mv RSEM datatypes to separate repository, remove samtools dependency
author Jim Johnson <jj@umn.edu>
date Mon, 10 Mar 2014 07:19:56 -0500
parents ca988deacfd1
children 30a8343fb0e7
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2:5949673f9e3e 3:59459de65740
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.17">rsem</requirement> 4 <requirement type="package" version="1.1.17">rsem</requirement>
5 <requirement type="package" version="1.0.0">bowtie</requirement> 5 <requirement type="package" version="1.0.0">bowtie</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command>
8 echo $reference_name " " | tee $reference_file &amp;&amp;
8 mkdir $reference_file.extra_files_path &amp;&amp; 9 mkdir $reference_file.extra_files_path &amp;&amp;
9 cd $reference_file.extra_files_path &amp;&amp; 10 cd $reference_file.extra_files_path &amp;&amp;
10 rsem-prepare-reference 11 rsem-prepare-reference
11 #if $polya.polya_use == 'add': 12 #if $polya.polya_use == 'add':
12 #if $polya.polya_length: 13 #if $polya.polya_length:
29 #else: 30 #else:
30 --gtf $reference.gtf 31 --gtf $reference.gtf
31 $reference.reference_fasta_file 32 $reference.reference_fasta_file
32 #end if 33 #end if
33 $reference_name 34 $reference_name
35 > ${reference_name}.log
34 </command> 36 </command>
35 <inputs> 37 <inputs>
36 <conditional name="reference"> 38 <conditional name="reference">
37 <param name="ref_type" type="select" label="Reference transcript source"> 39 <param name="ref_type" type="select" label="Reference transcript source">
38 <option value="transcripts">transcript fasta</option> 40 <option value="transcripts">transcript fasta</option>
59 If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file. 61 If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file.
60 Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene. 62 Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene.
61 </help> 63 </help>
62 </param> 64 </param>
63 <param name="reference_name" type="text" value="rsem_ref_name" label="reference name"> 65 <param name="reference_name" type="text" value="rsem_ref_name" label="reference name">
64 <help>A one work name for this RSEM reference containing only letters, digits, and underscore characters</help> 66 <help>A one word name for this RSEM reference containing only letters, digits, and underscore characters</help>
65 <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator> 67 <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator>
66 </param> 68 </param>
67 <conditional name="polya"> 69 <conditional name="polya">
68 <param name="polya_use" type="select" label="PolyA "> 70 <param name="polya_use" type="select" label="PolyA ">
69 <option value="add" selected="true">Add poly(A) tails to all transcripts</option> 71 <option value="add" selected="true">Add poly(A) tails to all transcripts</option>