Mercurial > repos > saharlcc > isoem2_isode2
comparison isoem2_isode2/isoem_wrapper.xml @ 10:78d03bf22a1f draft
- Add prinseq command to filter RNA-Seq data
- Fix in interpreting p-value when replicates are used
author | saharlcc |
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date | Thu, 16 Mar 2017 13:44:03 -0400 |
parents | |
children | be08c88b353e |
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9:ce0a125b3cd1 | 10:78d03bf22a1f |
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1 <tool id="isoem" name="IsoEM2" version="1.0.0"> | |
2 <description> Infers isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data</description> | |
3 <requirements> | |
4 | |
5 </requirements> | |
6 <command interpreter="bash"> | |
7 isoem_wrapper.sh | |
8 | |
9 ## Provide outputs. | |
10 --out_gene_fpkm $out_gene_fpkm | |
11 --out_gene_tpm $out_gene_tpm | |
12 --out_iso_fpkm $out_iso_fpkm | |
13 --out_iso_tpm $out_iso_tpm | |
14 --out_bootstrap $out_bootstrap | |
15 | |
16 --MinReadLength $MinReadLength | |
17 | |
18 ## Handle reference file . | |
19 #if $referenceSource.CCDSsource == "history": | |
20 --fastaFile $referenceSource.fastaFile | |
21 #else: | |
22 --GTF $referenceSource.index.fields.GTF --TMAP_INDEX $referenceSource.index.fields.TMAP_INDEX --HISAT2_INDEX $referenceSource.index.fields.HISAT2_INDEX --Cluster $referenceSource.index.fields.Cluster | |
23 #end if | |
24 | |
25 ## First input file always required fastq1. | |
26 --input1 $Data.input1 | |
27 | |
28 ## Set params based on whether reads are single-end or paired. | |
29 #if $Data.RNAseqType == "Illumina-paired-end": | |
30 --input2 $Data.input2 | |
31 #else: | |
32 -m $Data.lengthMean | |
33 -d $Data.lengthSd | |
34 #end if | |
35 | |
36 ## RNA-Seq type based on sequencing platform. | |
37 --RNA_type $Data.RNAseqType > $Run 2>&1 | |
38 | |
39 | |
40 | |
41 </command> | |
42 <inputs> | |
43 <conditional name="referenceSource"> | |
44 <param name="CCDSsource" type="select" label="Will you upload a reference transcriptome fasta file from your history or use a built-in reference?" help="Built-ins were indexed using default options"> | |
45 <option value="indexed">Use a built-in reference</option> | |
46 <option value="history">Use reference from the history</option> | |
47 </param> | |
48 <when value="indexed"> | |
49 <param name="index" type="select" label="Select a reference dataset" help="If your reference of interest is not listed, contact the Galaxy team"> | |
50 <options from_data_table="IsoEM" /> | |
51 </param> | |
52 </when> | |
53 <when value="history"> | |
54 <param name="fastaFile" type="data" format="fasta" metadata_name="dbkey" label="Select CCDS fasta file from your history" /> | |
55 </when> <!-- history --> | |
56 </conditional> <!-- referenceSource --> | |
57 <conditional name="Data"> | |
58 <!-- | |
59 <param name="sPaired" type="select" label="Is this library Single-end or Paired-end?"> | |
60 <option value="single">Single-end</option> | |
61 <option value="paired">Paired-end</option> | |
62 </param> | |
63 --> | |
64 <param name="RNAseqType" type="select" label="Select RNA-seq type"> | |
65 <option value="Ion-Torrent-Proton">Ion Torrent single-end</option> | |
66 <option value="Illumina-paired-end">Illumina paired-end</option> | |
67 <option value="Illumina-single-end">Illumina single-end</option> | |
68 </param> <!-- RNAseqType --> | |
69 <when value="Illumina-paired-end"> | |
70 <param name="input1" type="data" label="RNA-Seq file1, fastq or bam format" /> | |
71 <param name="input2" type="data" label="RNA-Seq file2, fastq or bam format" /> | |
72 </when> | |
73 <when value="Ion-Torrent-Proton"> | |
74 <param name="input1" type="data" label="RNA-Seq file, fastq or bam format" /> | |
75 <param name="lengthMean" type="text" label="m (RNA-Seq fragment length mean)" /> | |
76 <param name="lengthSd" type="text" label="d (RNA-Seq fragment length standard deviation)" /> | |
77 </when> | |
78 <when value="Illumina-single-end"> | |
79 <param name="input1" type="data" label="RNA-Seq file, fastq or bam format" /> | |
80 <param name="lengthMean" type="text" label="m (RNA-Seq fragment length mean)" /> | |
81 <param name="lengthSd" type="text" label="d (RNA-Seq fragment length standard deviation)" /> | |
82 </when> | |
83 </conditional> <!-- Data --> | |
84 | |
85 <param name="MinReadLength" label="Min. read length" type="text" value="50" /> | |
86 | |
87 | |
88 <!-- | |
89 <param name="RNAseqType" type="select" label="Select RNA-seq type"> | |
90 <option value="Ion-Torrent-Proton">Ion Torrent Proton</option> | |
91 <option value="Illumina-paired-end">Illumina paired-end</option> | |
92 <option value="Illumina-single-end">Illumina single-end</option> | |
93 </param> | |
94 --> | |
95 </inputs> | |
96 <outputs> | |
97 <data name="out_gene_fpkm" format="tabular" label="Gene_fpkm"/> | |
98 <data name="out_gene_tpm" format="tabular" label="Gene_tpm"/> | |
99 <data name="out_iso_fpkm" format="tabular" label="Iso_fpkm"/> | |
100 <data name="out_iso_tpm" format="tabular" label="Iso_tpm"/> | |
101 <data name="out_bootstrap" format="toolshed.gz" label="Bootstrap.tar.gz"/> | |
102 <data name="Run" format="log" label="isoem_wrapper: The log file" /> | |
103 </outputs> | |
104 <help> | |
105 **What it does** | |
106 | |
107 * The IsoEM can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. | |
108 | |
109 **Input Format** | |
110 | |
111 * The tool accept the fastq, fastq.gz, bam formats. Extension must be specified at the end of the file names. | |
112 * RNA-seq data must be Ion Torrent Proton or Illumina sequncing data. | |
113 | |
114 ----- | |
115 | |
116 | |
117 **Output Format** | |
118 | |
119 * Four output files containinag results for **Gene FPKM**, **Gene TPM**, **Isoform FPKM**, and **Isoform TPM**. The four files have identical format with the following fields. | |
120 | |
121 | |
122 * 1 Gene/Isoform ID | |
123 * 2 Gene/Isoform FPKM (Fragments Per Kilobase per Million reads) or TPM (Transcripts per Million reads) | |
124 * 3 Min FPKM/TPM | |
125 * 4 Max FPKM/TPM | |
126 | |
127 * And one compressed **Bootstrap.tar** file will be used in IsoDE2 to compute gene differential expression. | |
128 </help> | |
129 | |
130 | |
131 </tool> | |
132 | |
133 | |
134 | |
135 |