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annotate rsem_prepare_reference.xml @ 3:d7d4d662b0e9 default tip
Add test output assertion in rsem_prepare_reference.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 07 Feb 2014 06:54:54 -0600 |
| parents | f6b8155ab12a |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="rsem_prepare_reference" name="RSEM prepare reference" version="1.1.17"> |
| 2 <description></description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.1.17">rsem</requirement> | |
| 5 <requirement type="package" version="1.0.0">bowtie</requirement> | |
| 6 </requirements> | |
| 7 <command> | |
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1ff2fc8da328
Updates to rsem_calculate_expression.xml
Jim Johnson <jj@umn.edu>
parents:
0
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changeset
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8 mkdir $reference_file.extra_files_path && |
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1ff2fc8da328
Updates to rsem_calculate_expression.xml
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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9 cd $reference_file.extra_files_path && |
| 0 | 10 rsem-prepare-reference |
| 11 #if $polya.polya_use == 'add': | |
| 12 #if $polya.polya_length: | |
| 13 --polyA-length $polya.polya_length | |
| 14 #end if | |
| 15 #elif $polya.polya_use == 'subset': | |
| 16 --no-polyA-subset $polya.no_polya_subset | |
| 17 #if $polya.polya_length: | |
| 18 --polyA-length $polya.polya_length | |
| 19 #end if | |
| 20 #elif $polya.polya_use == 'none': | |
| 21 --no-polyA | |
| 22 #end if | |
| 23 $ntog | |
| 24 #if $transcript_to_gene_map: | |
| 25 --transcript-to-gene-map $transcript_to_gene_map | |
| 26 #end if | |
| 27 #if $reference.ref_type == 'transcripts': | |
| 28 $reference.reference_fasta_file | |
| 29 #else: | |
| 30 --gtf $reference.gtf | |
| 31 $reference.reference_fasta_file | |
| 32 #end if | |
| 33 $reference_name | |
| 34 </command> | |
| 35 <inputs> | |
| 36 <conditional name="reference"> | |
| 2 | 37 <param name="ref_type" type="select" label="Reference transcript source"> |
| 0 | 38 <option value="transcripts">transcript fasta</option> |
| 39 <option value="genomic">reference genome and gtf</option> | |
| 40 </param> | |
| 41 <when value="transcripts"> | |
| 42 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" | |
| 43 help="The files should contain the sequences of transcripts."/> | |
| 44 </when> | |
| 45 <when value="genomic"> | |
| 46 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" | |
| 2 | 47 help="The file should contain the sequence of an entire genome."/> |
| 48 <param name="gtf" type="data" format="gtf" label="gtf" | |
| 0 | 49 help="extract transcript reference sequences using the gene annotations specified in this GTF" /> |
| 50 </when> | |
| 51 </conditional> | |
| 52 <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" > | |
| 53 <help> | |
| 54 Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character ) | |
| 55 The map can be obtained from the UCSC table browser | |
| 56 group: Genes and Gene Prediction Tracks | |
| 57 table: knownIsoforms | |
| 58 Without a map: | |
| 59 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. | |
| 61 </help> | |
| 62 </param> | |
| 2 | 63 <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> | |
| 65 <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator> | |
| 0 | 66 </param> |
| 67 <conditional name="polya"> | |
| 68 <param name="polya_use" type="select" label="PolyA "> | |
| 69 <option value="add" selected="true">Add poly(A) tails to all transcripts</option> | |
| 70 <option value="subset">Exclude poly(A) tails from selected transcripts</option> | |
| 71 <option value="none">Do not add poly(A) tails to any transcripts</option> | |
| 72 </param> | |
| 73 <when value="add"> | |
| 74 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)"> | |
| 75 <validator type="in_range" message="must be positive " min="1"/> | |
| 76 </param> | |
| 77 </when> | |
| 78 <when value="subset"> | |
| 79 <param name="no_polya_subset" type="data" format="tabular" optional="true" label="List of transcript IDs (one per line) that should should not have polyA tails added."/> | |
| 80 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)"> | |
| 81 <validator type="in_range" message="must be positive " min="1"/> | |
| 82 </param> | |
| 83 </when> | |
| 84 <when value="none"/> | |
| 85 </conditional> | |
| 86 <param name="ntog" type="boolean" truevalue="--no-ntog" falsevalue="" checked="false" label="Disable the conversion of 'N' characters to 'G' characters in the reference sequences" help="Bowite uses the automatic N to G conversion to to align against all positions in the reference."/> | |
| 87 </inputs> | |
| 88 <stdio> | |
| 89 <exit_code range="1:" level="fatal" description="Error Running RSEM" /> | |
| 90 </stdio> | |
| 91 <outputs> | |
| 92 <data format="rsem_ref" name="reference_file" label="RSEM ${reference_name} reference"/> | |
| 93 </outputs> | |
| 2 | 94 <tests> |
| 95 <test> | |
| 96 <param name="ref_type" value="genomic"/> | |
| 97 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/> | |
| 98 <param name="gtf" value="ref.gtf" ftype="gtf"/> | |
| 99 <param name="reference_name" value="ref"/> | |
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d7d4d662b0e9
Add test output assertion in rsem_prepare_reference.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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100 <output name="rsem_ref"> |
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d7d4d662b0e9
Add test output assertion in rsem_prepare_reference.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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101 <assert_contents> |
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d7d4d662b0e9
Add test output assertion in rsem_prepare_reference.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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102 <has_text text="ref.grp" /> |
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d7d4d662b0e9
Add test output assertion in rsem_prepare_reference.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
103 </assert_contents> |
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d7d4d662b0e9
Add test output assertion in rsem_prepare_reference.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
|
104 </output> |
| 2 | 105 </test> |
| 106 </tests> | |
| 0 | 107 <help> |
| 108 | |
| 109 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/ | |
| 110 | |
| 111 NAME | |
| 112 rsem-prepare-reference | |
| 113 | |
| 114 SYNOPSIS | |
| 115 rsem-prepare-reference [options] reference_fasta_file(s) reference_name | |
| 116 | |
| 117 DESCRIPTION | |
| 118 The rsem-prepare-reference program extracts/preprocesses the reference sequences and builds Bowtie indices using default parameters. | |
| 119 This program is used in conjunction with the 'rsem-calculate-expression' program. | |
| 120 | |
| 121 INPUTS | |
| 2 | 122 A fasta file of transcripts |
| 123 or | |
| 124 A genome sequence fasta file and a GTF gene annotation file. (When using UCSC data, include the related knownIsoforms.txt) | |
| 0 | 125 |
| 126 </help> | |
| 127 </tool> |