Mercurial > repos > trinity_ctat > align_and_estimate_abundance
annotate align_and_estimate_abundance.xml @ 16:e27d87a63bb2 draft default tip
Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.
| author | trinity_ctat |
|---|---|
| date | Fri, 06 Oct 2017 10:58:53 -0400 |
| parents | 6e1eb00bfa53 |
| children |
| rev | line source |
|---|---|
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16
e27d87a63bb2
Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.
trinity_ctat
parents:
14
diff
changeset
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1 <tool id="RSEM_abundance_estimation" name="align_and_estimate_abundance" version="1.0.0" profile="17.05"> |
| 0 | 2 |
| 3 <description>run RSEM to estimate transcript abundances</description> | |
| 4 | |
| 5 <requirements> | |
| 6 <requirement type="package" version="2.7">python</requirement> | |
| 13 | 7 <requirement type="package" version="1.3.0">rsem</requirement> |
| 0 | 8 <requirement type="package" version="2.4.0">trinity</requirement> |
| 9 </requirements> | |
| 10 | |
|
16
e27d87a63bb2
Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.
trinity_ctat
parents:
14
diff
changeset
|
11 <command detect_errors="exit_code"> |
| 0 | 12 <![CDATA[ |
| 13 | 13 python $__tool_directory__/trinityToolWrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie2 --trinity_mode --prep_reference --output_dir "subdir" |
| 0 | 14 |
| 15 ## Inputs. | |
| 16 #if str($inputs.paired_or_single) == "paired": | |
| 17 --left $inputs.left_input --right $inputs.right_input | |
| 18 #if $inputs.left_input.ext == 'fa': | |
| 19 --seqType fa | |
| 20 #else: | |
| 21 --seqType fq | |
| 22 #end if | |
| 23 #if str($inputs.library_type) != "None": | |
| 24 --SS_lib_type $inputs.library_type | |
| 25 #end if | |
| 26 | |
| 27 #else: | |
| 28 --single $inputs.input | |
| 29 #if str($inputs.input.ext) == 'fa': | |
| 30 --seqType fa | |
| 31 #else: | |
| 32 --seqType fq | |
| 33 #end if | |
| 34 #if str($inputs.library_type) != "None": | |
| 35 --SS_lib_type $inputs.library_type | |
| 36 #end if | |
| 37 #end if | |
| 38 ]]> | |
| 39 | |
| 40 </command> | |
| 41 <inputs> | |
| 42 <param format="fasta" name="transcripts" type="data" label="Transcripts Fasta" help="Fasta sequences against which reads are aligned. This may be the Assembled Transcripts file from Trinity." /> | |
| 43 | |
| 44 <conditional name="inputs"> | |
| 45 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> | |
| 46 <option value="paired">Paired</option> | |
| 47 <option value="single">Single</option> | |
| 48 </param> | |
| 49 <when value="paired"> | |
| 50 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> | |
| 51 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> | |
| 52 <param name="library_type" type="select" label="Strand-specific Library Type"> | |
| 53 <option value="None">None</option> | |
| 54 <option value="FR">FR</option> | |
| 55 <option value="RF">RF</option> | |
| 56 </param> | |
| 57 | |
| 58 </when> | |
| 59 <when value="single"> | |
| 60 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> | |
| 61 <param name="library_type" type="select" label="Strand-specific Library Type"> | |
| 62 <option value="None">None</option> | |
| 63 <option value="F">F</option> | |
| 64 <option value="R">R</option> | |
| 65 </param> | |
| 66 | |
| 67 </when> | |
| 68 </conditional> | |
| 69 </inputs> | |
| 70 | |
| 71 <outputs> | |
| 14 | 72 <data format="txt" name="transcript_counts" label="${tool.name} on ${on_string}: Isoform Counts" from_work_dir="subdir/RSEM.isoforms.results"/> |
| 73 <data format="txt" name="gene_counts" label="${tool.name} on ${on_string}: Gene counts" from_work_dir="subdir/RSEM.genes.results"/> | |
| 0 | 74 </outputs> |
| 75 | |
| 76 <tests> | |
| 77 <test> | |
| 78 <param name="transcripts" value="reads.simPE.Trinity.fasta" /> | |
| 79 <param name="paired_or_single" value="paired" /> | |
| 80 <param name="left_input" value="reads.left.simPE.fq" /> | |
| 81 <param name="right_input" value="reads.right.simPE.fq" /> | |
| 82 <param name="library_type" value="None" /> | |
| 83 | |
| 84 <output name="transcript_counts" > | |
| 85 <assert_contents> | |
| 86 <has_line_matching expression=".+" /> | |
| 87 <has_line line="transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct" /> | |
| 88 </assert_contents> | |
| 89 </output> | |
| 90 | |
| 91 <output name="gene_counts" > | |
| 92 <assert_contents> | |
| 93 <has_line_matching expression=".+" /> | |
| 94 <has_line line="gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM" /> | |
| 95 </assert_contents> | |
| 96 </output> | |
| 97 </test> | |
| 98 <test> | |
| 99 <param name="transcripts" value="Sp.Trinity.fasta" /> | |
| 100 <param name="paired_or_single" value="paired" /> | |
| 101 <param name="left_input" value="Sp_ds.left.fq" /> | |
| 102 <param name="right_input" value="Sp_ds.right.fq" /> | |
| 103 <param name="library_type" value="None" /> | |
| 104 | |
| 105 <output name="transcript_counts" > | |
| 106 <assert_contents> | |
| 107 <has_line_matching expression=".+" /> | |
| 108 <has_line line="transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct" /> | |
| 109 </assert_contents> | |
| 110 </output> | |
| 111 | |
| 112 <output name="gene_counts" > | |
| 113 <assert_contents> | |
| 114 <has_line_matching expression=".+" /> | |
| 115 <has_line line="gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM" /> | |
| 116 </assert_contents> | |
| 117 </output> | |
| 118 </test> | |
| 119 <test> | |
| 120 <param name="transcripts" value="Sp.Trinity.fasta" /> | |
| 121 <param name="paired_or_single" value="paired" /> | |
| 122 <param name="left_input" value="Sp_hs.left.fq" /> | |
| 123 <param name="right_input" value="Sp_hs.right.fq" /> | |
| 124 <param name="library_type" value="None" /> | |
| 125 | |
| 126 <output name="transcript_counts" > | |
| 127 <assert_contents> | |
| 128 <has_line_matching expression=".+" /> | |
| 129 <has_line line="transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct" /> | |
| 130 </assert_contents> | |
| 131 </output> | |
| 132 | |
| 133 <output name="gene_counts" > | |
| 134 <assert_contents> | |
| 135 <has_line_matching expression=".+" /> | |
| 136 <has_line line="gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM" /> | |
| 137 </assert_contents> | |
| 138 </output> | |
| 139 </test> | |
| 140 </tests> | |
| 141 | |
| 142 <help> | |
| 143 .. class:: infomark | |
| 144 | |
| 145 Use RSEM to generate transcript quantification for genes and isoforms. | |
| 146 | |
| 147 To learn more about RSEM read their paper_ or visit their website_. | |
| 148 | |
| 149 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols publication_ . | |
| 150 | |
| 151 .. _paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323 | |
| 152 .. _publication: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html | |
| 153 .. _website: http://deweylab.biostat.wisc.edu/rsem/README.html | |
| 154 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki | |
| 155 </help> | |
| 156 | |
| 157 <citations> | |
| 158 <citation type="doi">10.1038/nbt.1883</citation> | |
| 159 </citations> | |
| 160 | |
| 161 </tool> |