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author devteam
date Thu, 23 Jan 2014 12:31:27 -0500
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1 <tool id="express" name="eXpress" version="1.1.1">
2 <description>Quantify the abundances of a set of target sequences from sampled subsequences</description>
3 <requirements>
4 <requirement type="package" version="1.1.1">eXpress</requirement>
5 </requirements>
6 <command>
7 express --no-update-check
8 ## Additional parameters.
9 #if $additional_params.use_additional == "yes":
10 -B $additional_params.additional_batch
11 -O $additional_params.additional_online
12
13 #if str( $additional_params.calc_covar ) == 'yes':
14 --calc-covar
15 #end if
16
17 -m $additional_params.mean_fragment_length
18
19 -s $additional_params.fragment_length_deviation
20 #end if
21
22 ## Input files
23 $multiFasta
24 $bamOrSamFile
25 </command>
26 <inputs>
27 <param format="fasta" name="multiFasta" type="data" label="A set of target references (annotation) in multi-FASTA format" help="The multi-FASTA file can also be a fasta file." />
28 <param format="sam,bam" name="bamOrSamFile" type="data" label="Alignments in the BAM or SAM format" help="The set of aligned reads." />
29 <conditional name="additional_params">
30 <param name="use_additional" type="select" label="Use Additional Parameters?">
31 <option value="no">No</option>
32 <option value="yes">Yes</option>
33 </param>
34 <when value="no">
35 </when>
36 <when value="yes">
37 <param name="additional_batch" type="integer" label="Additional batch EM rounds" value="0" help="0 is default. Can improve accuracy at the cost of time."/>
38 <param name="additional_online" type="integer" label="Additional online EM rounds" value="0" help="0 is default. Can improve accuracy at the cost of time."/>
39 <param name="calc_covar" type="select" label="Calculate the covariance between targets and outputs?" help="This calculation requires slightly more time and memory.">
40 <option value="no">No</option>
41 <option value="yes">Yes</option>
42 </param>
43 <param name="mean_fragment_length" type="integer" label="Specifies the mean fragment length" value="200" help="200 is default. While the empirical distribution is estimated from paired-end reads on-the-fly, this value paramaterizes the prior distribution."/>
44 <param name="fragment_length_deviation" type="integer" label="Specified the fragment length standard deviation" value="60" help="60 is default. While the empirical distribution is estimated from paired-end reads on-the-fly, this value paramaterizes the prior distribution."/>
45 </when>
46 </conditional>
47 </inputs>
48 <outputs>
49 <data format="txt" name="params" from_work_dir="params.xprs"/>
50 <data format="txt" name="results" from_work_dir="results.xprs"/>
51 <data format="txt" name="varcov" from_work_dir="varcov.xprs">
52 <filter>additional_params[ 'use_additional' ] == "yes" and additional_params[ 'calc_covar' ] == "yes"</filter>
53 </data>
54 </outputs>
55
56 <tests>
57 <!-- Test for the most simple case : Running eXpress with a .bam file and a .fasta file -->
58 <test>
59 <!-- TopHat commands:
60 eXpress Trinity.fasta hits.bam
61 -->
62 <param name="bamOrSamFile" ftype="bam" value="eXpress_hits.bam"/>
63 <param name="multiFasta" ftype="fasta" value="eXpress_Trinity.fasta"/>
64 <param name="use_additional" value="no"/>
65
66 <output name="params" file="eXpress_params.xprs" lines_diff="300"/>
67 <output name="results" file="eXpress_results.xprs" lines_diff="10"/>
68 </test>
69 <!-- Test for an other simple case : Running eXpress with a .sam file and a .fasta file -->
70 <test>
71 <!-- TopHat commands:
72 eXpress Trinity.fasta hits.sam
73 -->
74 <param name="bamOrSamFile" ftype="sam" value="eXpress_hits.sam"/>
75 <param name="multiFasta" ftype="fasta" value="eXpress_Trinity.fasta"/>
76 <param name="use_additional" value="no"/>
77
78 <output name="params" file="eXpress_params_sam.xprs" lines_diff="300"/>
79 <output name="results" file="eXpress_results_sam.xprs" lines_diff="10"/>
80 </test>
81 <!-- Test for a complex case : All the parameters has been activated and modified -->
82 <test>
83 <!-- TopHat commands: eXpress -B 1 -O 1 ++calc-covar -m 300 -s 85 Trinity.fasta hits.sam -->
84 <param name="bamOrSamFile" ftype="sam" value="eXpress_hits_all_params.bam"/>
85 <param name="multiFasta" ftype="fasta" value="eXpress_Trinity_all_params.fasta"/>
86
87 <param name="use_additional" value="yes"/>
88 <param name="additional_batch" value="1"/>
89 <param name="additional_online" value="1" />
90 <param name="calc_covar" value="yes"/>
91 <param name="mean_fragment_length" value="300"/>
92 <param name="fragment_length_deviation" value="85"/>
93
94 <output name="params" file="eXpress_params_all_params.xprs" lines_diff="300"/>
95 <output name="results" file="eXpress_results_all_params.xprs" lines_diff="10"/>
96 <output name="varcov" file="eXpress_varcov_all_params.xprs"/>
97 </test>
98 </tests>
99 <help>
100 **eXpress Overview**
101
102 eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data.
103
104 .. _Ensembl: http://bio.math.berkeley.edu/eXpress/
105
106 -----
107
108 **Input format**
109
110 eXpress requires two input files:
111
112 - A multi-FASTA file containing the transcript sequences.
113 - Read alignments to the multi-FASTA file in BAM or SAM format.
114
115 ------
116
117 **Outputs**
118
119 - The output for eXpress is saved in a file called results.xprs in an easy-to-parse tab-delimited format.
120
121 - Also, params.xprs contains the values of the other parameters (besides abundances and counts) estimated by eXpress.
122
123 - If you choose to use to calculate the covariance between targets and outputs, an other output would be : varcov.xprs.
124 </help>
125 </tool>