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comparison align_and_estimate_abundance.xml @ 2:de0af39266ef draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
author iuc
date Mon, 25 Apr 2016 10:02:37 -0400
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children c7555bc21812
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1:0067c78f49dc 2:de0af39266ef
1 <tool id="align_and_estimate_abundance" name="Align reads and estimate abundance" version="2.1.1">
2 <description>on a de novo assembly of RNA-Seq data</description>
3 <requirements>
4 <requirement type="package" version="2.1.1">trinity</requirement>
5 <requirement type="package" version="1.1.2">bowtie</requirement>
6 <requirement type="package" version="2.2.6">bowtie2</requirement>
7 <requirement type="package" version="1.2">samtools</requirement>
8 <requirement type="package" version="1.2.28">rsem</requirement>
9 <requirement type="package" version="1.5.1">express</requirement>
10 </requirements>
11 <stdio>
12 <exit_code range="1:"/>
13 </stdio>
14 <command><![CDATA[
15 ln -s $transcripts input.fa
16
17 &&
18
19 align_and_estimate_abundance.pl
20
21 --transcripts input.fa
22
23 --est_method $method.est_method
24 #if $method.est_method == "RSEM" or $method.est_method == "eXpress":
25 --aln_method $method.aln_method
26 #end if
27
28 #if $inputs.paired_or_single == "paired":
29 --left $inputs.left_input --right $inputs.right_input
30
31 #if $inputs.left_input.is_of_type('fasta'):
32 --seqType fa
33 #else:
34 --seqType fq
35 #end if
36
37 #if $inputs.strand.is_strand_specific:
38 --SS_lib_type $inputs.strand.library_type
39 #end if
40
41 #else:
42 --single $inputs.input
43
44 #if $inputs.input.is_of_type('fasta'):
45 --seqType fa
46 #else:
47 --seqType fq
48 #end if
49
50 #if $inputs.strand.is_strand_specific:
51 --SS_lib_type $inputs.strand.library_type
52 #end if
53 #end if
54
55 --max_ins_size $inputs.paired_fragment_length
56
57 ## Additional parameters.
58 #if $additional_params.gene_map.has_gene_map == "yes":
59 --gene_trans_map $additional_params.gene_map.gene_trans_map
60 #else
61 --trinity_mode
62 #end if
63
64 --prep_reference
65
66 --output_dir .
67
68 ## CPU
69 --thread_count \${GALAXY_SLOTS:-4}
70 ]]></command>
71 <inputs>
72 <param format="fasta" name="transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/>
73 <conditional name="inputs">
74 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
75 <option value="paired">Paired</option>
76 <option value="single">Single</option>
77 </param>
78 <when value="paired">
79 <param format="fasta,fastqsanger" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
80 <param format="fasta,fastqsanger" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
81 <conditional name="strand">
82 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
83 <when value="false">
84 </when>
85 <when value="true">
86 <param name="library_type" type="select" label="Strand-specific Library Type">
87 <option value="FR">Forward-Reverse</option>
88 <option value="RF">Reverse-Forward</option>
89 </param>
90 </when>
91 </conditional>
92 <param name="paired_fragment_length" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/>
93 </when>
94 <when value="single">
95 <param format="fasta,fastqsanger" name="input" type="data" label="Single-end reads" help=""/>
96 <conditional name="strand">
97 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
98 <when value="false">
99 </when>
100 <when value="true">
101 <param name="library_type" type="select" label="Strand-specific Library Type">
102 <option value="F">F</option>
103 <option value="R">R</option>
104 </param>
105 </when>
106 </conditional>
107 </when>
108 </conditional>
109
110 <conditional name="method">
111 <param type="select" name="est_method" label="Abundance estimation method">
112 <option value="RSEM">RSEM</option>
113 <option value="eXpress">eXpress</option>
114 </param>
115 <when value="RSEM">
116 <param type="select" name="aln_method" label="Alignment method">
117 <option value="bowtie">Bowtie</option>
118 <option value="bowtie2">Bowtie2</option>
119 </param>
120 </when>
121 <when value="eXpress">
122 <param type="select" name="aln_method" label="Alignment method">
123 <option value="bowtie">Bowtie</option>
124 <option value="bowtie2">Bowtie2</option>
125 </param>
126 </when>
127 </conditional>
128
129 <section name="additional_params" title="Additional Options" expanded="False">
130 <conditional name="gene_map">
131 <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed">
132 <option value="no">No</option>
133 <option value="yes">Yes</option>
134 </param>
135 <when value="no">
136 </when>
137 <when value="yes">
138 <param format="tabular" name="gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />
139 </when>
140 </conditional>
141
142 </section>
143 </inputs>
144 <outputs>
145 <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="RSEM.isoforms.results">
146 <filter>method['est_method'] == "RSEM"</filter>
147 </data>
148 <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="RSEM.genes.results">
149 <filter>method['est_method'] == "RSEM"</filter>
150 </data>
151
152 <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="results.xprs">
153 <filter>method['est_method'] == "eXpress"</filter>
154 </data>
155 <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="results.xprs.genes">
156 <filter>method['est_method'] == "eXpress"</filter>
157 </data>
158 </outputs>
159 <tests>
160 <test>
161 <param name="paired_or_single" value="paired"/>
162 <param name="left_input" value="reads.left.fq"/>
163 <param name="right_input" value="reads.right.fq"/>
164 <param name="transcripts" value="raw/Trinity.fasta"/>
165 <param name="library_type" value="RF"/>
166 <param name="est_method" value="RSEM"/>
167 <param name="aln_method" value="bowtie"/>
168 <param name="has_gene_map" value="no"/>
169 <output name="isoforms_counts_rsem">
170 <assert_contents>
171 <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
172 <has_n_columns n="8" />
173 </assert_contents>
174 </output>
175 <output name="genes_counts_rsem">
176 <assert_contents>
177 <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" />
178 <has_n_columns n="7" />
179 </assert_contents>
180 </output>
181 </test>
182 <test>
183 <param name="paired_or_single" value="paired"/>
184 <param name="left_input" value="reads.left.fq"/>
185 <param name="right_input" value="reads.right.fq"/>
186 <param name="transcripts" value="raw/Trinity.fasta"/>
187 <param name="library_type" value="RF"/>
188 <param name="est_method" value="RSEM"/>
189 <param name="aln_method" value="bowtie2"/>
190 <param name="has_gene_map" value="no"/>
191 <output name="isoforms_counts_rsem">
192 <assert_contents>
193 <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
194 <has_n_columns n="8" />
195 </assert_contents>
196 </output>
197 <output name="genes_counts_rsem">
198 <assert_contents>
199 <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" />
200 <has_n_columns n="7" />
201 </assert_contents>
202 </output>
203 </test>
204 <test>
205 <param name="paired_or_single" value="paired"/>
206 <param name="left_input" value="reads.left.fq"/>
207 <param name="right_input" value="reads.right.fq"/>
208 <param name="transcripts" value="raw/Trinity.fasta"/>
209 <param name="library_type" value="RF"/>
210 <param name="est_method" value="eXpress"/>
211 <param name="aln_method" value="bowtie"/>
212 <param name="has_gene_map" value="no"/>
213 <output name="isoforms_counts_express">
214 <assert_contents>
215 <has_line_matching expression=".*&#009;TRINITY_DN2_c3_g1_i1&#009;.*" />
216 <has_n_columns n="15" />
217 </assert_contents>
218 </output>
219 <output name="genes_counts_express">
220 <assert_contents>
221 <has_line_matching expression="NA&#009;TRINITY_DN3_c0_g1.*" />
222 <has_n_columns n="15" />
223 </assert_contents>
224 </output>
225 </test>
226 </tests>
227 <help>
228 <![CDATA[
229 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
230 This tool estimates the abundance of isoforms and genes of a transcriptome assembled with Trinity, using FastQ of a specific sample.
231
232 **Inputs**
233
234 It takes as input a transcriptome assembled with Trinity and the reads from a RNASeq sample.
235 You have to choose between several counting methods.
236
237 If you dont align on a Trinity assembly, you need to provide a file of the following (tabular) format to map gene ids to transcript ids:
238
239 =========== ================
240 gene1 transcript1
241 ----------- ----------------
242 gene2 transcript2
243 =========== ================
244
245 **Output**
246
247 This tool will produce 2 tabular files, with counts for isoforms and genes respectively. More details on this page:
248
249 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
250
251
252 .. _Trinity: http://trinityrnaseq.github.io
253 ]]>
254 </help>
255
256 <citations>
257 <citation type="doi">doi:10.1038/nbt.1883</citation>
258 </citations>
259 </tool>
260