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Upload ctat tools.
author trinity_ctat
date Tue, 17 Jul 2018 11:48:59 -0400
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1 <tool id="ctat_rsem_align_and_estimate_abundance" name="ctat_rsem_align_and_estimate_abundance" version="1.0.0" profile="17.05">
2
3 <description>run RSEM to estimate transcript abundances</description>
4
5 <requirements>
6 <requirement type="package" version="2.7">python</requirement>
7 <requirement type="package">subprocess32</requirement>
8 <requirement type="package">bzip2</requirement>
9 <requirement type="package" version="1.3.0">rsem</requirement>
10 <requirement type="package" version="3">bioconductor-edger</requirement>
11 <requirement type="package" version="2">bioconductor-qvalue</requirement>
12 <requirement type="package" version="2.6.6">trinity</requirement>
13 </requirements>
14
15 <command detect_errors="exit_code">
16 <![CDATA[
17 python $__tool_directory__/ctat_trinity_tool_wrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie2 --trinity_mode --prep_reference --output_dir "subdir"
18
19 ## Inputs.
20 #if str($inputs.paired_or_single) == "paired":
21 --left $inputs.left_input --right $inputs.right_input
22 #if $inputs.left_input.ext == 'fa':
23 --seqType fa
24 #else:
25 --seqType fq
26 #end if
27 #if str($inputs.library_type) != "None":
28 --SS_lib_type $inputs.library_type
29 #end if
30
31 #else:
32 --single $inputs.input
33 #if str($inputs.input.ext) == 'fa':
34 --seqType fa
35 #else:
36 --seqType fq
37 #end if
38 #if str($inputs.library_type) != "None":
39 --SS_lib_type $inputs.library_type
40 #end if
41 #end if
42 ]]>
43
44 </command>
45 <inputs>
46 <param format="fasta" name="transcripts" type="data" label="Transcripts Fasta" help="Fasta sequences against which reads are aligned. This may be the Assembled Transcripts file from Trinity." />
47
48 <conditional name="inputs">
49 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
50 <option value="paired">Paired</option>
51 <option value="single">Single</option>
52 </param>
53 <when value="paired">
54 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
55 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
56 <param name="library_type" type="select" label="Strand-specific Library Type">
57 <option value="None">None</option>
58 <option value="FR">FR</option>
59 <option value="RF">RF</option>
60 </param>
61
62 </when>
63 <when value="single">
64 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
65 <param name="library_type" type="select" label="Strand-specific Library Type">
66 <option value="None">None</option>
67 <option value="F">F</option>
68 <option value="R">R</option>
69 </param>
70
71 </when>
72 </conditional>
73 </inputs>
74
75 <outputs>
76 <data format="txt" name="transcript_counts" label="${tool.name} on ${on_string}: Isoform Counts" from_work_dir="subdir/RSEM.isoforms.results"/>
77 <data format="txt" name="gene_counts" label="${tool.name} on ${on_string}: Gene counts" from_work_dir="subdir/RSEM.genes.results"/>
78 </outputs>
79
80 <tests>
81 <test>
82 <param name="transcripts" value="reads.simPE.Trinity.fasta" />
83 <param name="paired_or_single" value="paired" />
84 <param name="left_input" value="reads.left.simPE.fq" />
85 <param name="right_input" value="reads.right.simPE.fq" />
86 <param name="library_type" value="None" />
87
88 <output name="transcript_counts" >
89 <assert_contents>
90 <has_line_matching expression=".+" />
91 <has_line line="transcript_id&#009;gene_id&#009;length&#009;effective_length&#009;expected_count&#009;TPM&#009;FPKM&#009;IsoPct" />
92 </assert_contents>
93 </output>
94
95 <output name="gene_counts" >
96 <assert_contents>
97 <has_line_matching expression=".+" />
98 <has_line line="gene_id&#009;transcript_id(s)&#009;length&#009;effective_length&#009;expected_count&#009;TPM&#009;FPKM" />
99 </assert_contents>
100 </output>
101 </test>
102 <test>
103 <param name="transcripts" value="Sp.Trinity.fasta" />
104 <param name="paired_or_single" value="paired" />
105 <param name="left_input" value="Sp_ds.left.fq" />
106 <param name="right_input" value="Sp_ds.right.fq" />
107 <param name="library_type" value="None" />
108
109 <output name="transcript_counts" >
110 <assert_contents>
111 <has_line_matching expression=".+" />
112 <has_line line="transcript_id&#009;gene_id&#009;length&#009;effective_length&#009;expected_count&#009;TPM&#009;FPKM&#009;IsoPct" />
113 </assert_contents>
114 </output>
115
116 <output name="gene_counts" >
117 <assert_contents>
118 <has_line_matching expression=".+" />
119 <has_line line="gene_id&#009;transcript_id(s)&#009;length&#009;effective_length&#009;expected_count&#009;TPM&#009;FPKM" />
120 </assert_contents>
121 </output>
122 </test>
123 <test>
124 <param name="transcripts" value="Sp.Trinity.fasta" />
125 <param name="paired_or_single" value="paired" />
126 <param name="left_input" value="Sp_hs.left.fq" />
127 <param name="right_input" value="Sp_hs.right.fq" />
128 <param name="library_type" value="None" />
129
130 <output name="transcript_counts" >
131 <assert_contents>
132 <has_line_matching expression=".+" />
133 <has_line line="transcript_id&#009;gene_id&#009;length&#009;effective_length&#009;expected_count&#009;TPM&#009;FPKM&#009;IsoPct" />
134 </assert_contents>
135 </output>
136
137 <output name="gene_counts" >
138 <assert_contents>
139 <has_line_matching expression=".+" />
140 <has_line line="gene_id&#009;transcript_id(s)&#009;length&#009;effective_length&#009;expected_count&#009;TPM&#009;FPKM" />
141 </assert_contents>
142 </output>
143 </test>
144 </tests>
145
146 <help>
147 .. class:: infomark
148
149 Use RSEM to generate transcript quantification for genes and isoforms.
150
151 To learn more about RSEM read their paper_ or visit their website_.
152
153 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols publication_ .
154
155 .. _paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323
156 .. _publication: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
157 .. _website: http://deweylab.biostat.wisc.edu/rsem/README.html
158 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
159 </help>
160
161 <citations>
162 <citation type="doi">10.1038/nbt.1883</citation>
163 </citations>
164
165 </tool>