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1 <tool id="RSEM_abundance_estimation" name="RSEM abundance estimation" version="0.0.2">
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2 <description>run RSEM to estimate transcript abundances</description>
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3 <requirements>
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4 <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
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5 <requirement type="package" version="1.1.17">rsem</requirement>
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6 </requirements>
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7 <command>
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8 \$TRINITY_HOME/util/RSEM_util/run_RSEM_align_n_estimate.pl --transcripts $transcripts
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9 ## Inputs.
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10 #if str($read_type.paired_or_single) == "single":
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11 #if $read_type.single_reads.extension.startswith( "fastq"):
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12 --seqType fq
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13 #else
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14 --seqType fa
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15 #end if
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16 --single $read_type.single_reads
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17 #else
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18 #if $read_type.left_reads.extension.startswith( "fastq"):
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19 --seqType fq
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20 #else
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21 --seqType fa
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22 #end if
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23 --left $read_type.left_reads
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24 --right $read_type.right_reads
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25 #end if
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26 #if $transcript.source == "other":
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27 --no_group_by_component
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28 --gene_trans_map $transcript.gene_trans_map
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29 #end if
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30 </command>
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31 <inputs>
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32 <param name="transcripts" type="data" format="fasta" label="transcripts_fasta" help="Fasta sequences for which reads are aligned." />
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33 <conditional name="read_type">
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34 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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35 <option value="paired">Paired</option>
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36 <option value="single">Single</option>
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37 </param>
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38 <when value="paired">
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39 <param name="left_reads" type="data" format="fasta,fastq" label="left reads" help="" />
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40 <param name="right_reads" type="data" format="fasta,fastq" label="right reads" help="" />
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41 <param name="ss_lib_type" type="select" label="strand-specific library type">
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42 <option value="RF">RF</option>
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43 <option value="FR">FR</option>
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44 </param>
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45 </when>
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46 <when value="single">
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47 <param name="single_reads" type="data" format="fasta,fastq" label="single reads" help="" />
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48 <param name="ss_lib_type" type="select" label="strand-specific library type">
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49 <option value="F">F</option>
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50 <option value="R">R</option>
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51 </param>
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52 </when>
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53 </conditional>
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54 <conditional name="transcript">
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55 <param name="source" type="select" label="Transcripts Source">
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56 <option value="trinity">Trinity</option>
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57 <option value="other">NOT trinity</option>
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58 </param>
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59 <when value="trinity"/>
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60 <when value="other">
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61 <param name="gene_trans_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" >
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62 <help>
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63 Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character )
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64 </help>
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65 </param>
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66 </when>
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67 </conditional>
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68 </inputs>
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69 <stdio>
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70 <exit_code range="1:" level="fatal" description="Error Running RSEM" />
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71 </stdio>
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72 <outputs>
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73 <data format="text" name="transcript_counts" label="${tool.name} on ${on_string}: Isoform Counts" from_work_dir="RSEM.isoforms.results"/>
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74 <data format="text" name="gene_counts" label="${tool.name} on ${on_string}: Gene counts" from_work_dir="RSEM.genes.results"/>
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75 </outputs>
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76 <tests>
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77 <test>
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78 <param name="target" value="trinity/Trinity.fasta" />
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79 <param name="aligner" value="bowtie" />
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80 <param name="paired_or_single" value="single" />
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81 <param name="library_type" value="None" />
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82 <param name="input" value="trinity/reads.left.fq" />
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83 </test>
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84 </tests>
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85 <help>
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86 .. _Trinity: http://trinityrnaseq.sourceforge.net
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87
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88 $TRINITY_HOME/util/RSEM_util/run_RSEM_align_n_estimate.pl --transcripts Trinity.fasta \
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89 --seqType fq --left left.reads.fq --right right.reads.fq
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90 </help>
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91 </tool>
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