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