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comparison align_and_estimate_abundance.xml @ 3:c7555bc21812 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
author iuc
date Tue, 03 May 2016 10:54:25 -0400
parents de0af39266ef
children e4a9e0798360
comparison
equal deleted inserted replaced
2:de0af39266ef 3:c7555bc21812
1 <tool id="align_and_estimate_abundance" name="Align reads and estimate abundance" version="2.1.1"> 1 <tool id="align_and_estimate_abundance" name="Align reads and estimate abundance" version="2.1.1.1">
2 <description>on a de novo assembly of RNA-Seq data</description> 2 <description>on a de novo assembly of RNA-Seq data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1.1">trinity</requirement> 4 <requirement type="package" version="2.1.1">trinity</requirement>
5 <requirement type="package" version="1.1.2">bowtie</requirement> 5 <requirement type="package" version="1.1.2">bowtie</requirement>
6 <requirement type="package" version="2.2.6">bowtie2</requirement> 6 <requirement type="package" version="2.2.6">bowtie2</requirement>
15 ln -s $transcripts input.fa 15 ln -s $transcripts input.fa
16 16
17 && 17 &&
18 18
19 align_and_estimate_abundance.pl 19 align_and_estimate_abundance.pl
20 20
21 --transcripts input.fa 21 --transcripts input.fa
22 22
23 --est_method $method.est_method 23 --est_method $method.est_method
24 #if $method.est_method == "RSEM" or $method.est_method == "eXpress": 24 #if $method.est_method == "RSEM" or $method.est_method == "eXpress":
25 --aln_method $method.aln_method 25 --aln_method $method.aln_method
26 #end if 26 #end if
27 27
28 #if $inputs.paired_or_single == "paired": 28 #if $inputs.paired_or_single == "paired":
29 --left $inputs.left_input --right $inputs.right_input 29 --left $inputs.left_input --right $inputs.right_input
30 30
31 #if $inputs.left_input.is_of_type('fasta'): 31 #if $inputs.left_input.is_of_type('fasta'):
32 --seqType fa 32 --seqType fa
33 #else: 33 #else:
34 --seqType fq 34 --seqType fq
35 #end if 35 #end if
36 36
37 #if $inputs.strand.is_strand_specific: 37 #if $inputs.strand.is_strand_specific:
38 --SS_lib_type $inputs.strand.library_type 38 --SS_lib_type $inputs.strand.library_type
39 #end if 39 #end if
40 40
41 #else: 41 #else:
42 --single $inputs.input 42 --single $inputs.input
43 43
44 #if $inputs.input.is_of_type('fasta'): 44 #if $inputs.input.is_of_type('fasta'):
45 --seqType fa 45 --seqType fa
46 #else: 46 #else:
47 --seqType fq 47 --seqType fq
48 #end if 48 #end if
49 49
50 #if $inputs.strand.is_strand_specific: 50 #if $inputs.strand.is_strand_specific:
51 --SS_lib_type $inputs.strand.library_type 51 --SS_lib_type $inputs.strand.library_type
52 #end if 52 #end if
53 #end if 53 #end if
54 54
55 --max_ins_size $inputs.paired_fragment_length 55 --max_ins_size $inputs.paired_fragment_length
56 56
57 ## Additional parameters. 57 ## Additional parameters.
58 #if $additional_params.gene_map.has_gene_map == "yes": 58 #if $additional_params.gene_map.has_gene_map == "no":
59 --gene_trans_map $additional_params.gene_map.gene_trans_map 59 --gene_trans_map $additional_params.gene_map.gene_trans_map
60 #else 60 #else
61 --trinity_mode 61 --trinity_mode
62 #end if 62 #end if
63 63
64 --prep_reference 64 --prep_reference
65 65
66 --output_dir . 66 --output_dir .
67 67
68 ## CPU 68 ## CPU
69 --thread_count \${GALAXY_SLOTS:-4} 69 --thread_count \${GALAXY_SLOTS:-4}
70 ]]></command> 70 ]]></command>
104 </param> 104 </param>
105 </when> 105 </when>
106 </conditional> 106 </conditional>
107 </when> 107 </when>
108 </conditional> 108 </conditional>
109 109
110 <conditional name="method"> 110 <conditional name="method">
111 <param type="select" name="est_method" label="Abundance estimation method"> 111 <param type="select" name="est_method" label="Abundance estimation method">
112 <option value="RSEM">RSEM</option> 112 <option value="RSEM">RSEM</option>
113 <option value="eXpress">eXpress</option> 113 <option value="eXpress">eXpress</option>
114 </param> 114 </param>
127 </conditional> 127 </conditional>
128 128
129 <section name="additional_params" title="Additional Options" expanded="False"> 129 <section name="additional_params" title="Additional Options" expanded="False">
130 <conditional name="gene_map"> 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"> 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="yes">Yes</option>
132 <option value="no">No</option> 133 <option value="no">No</option>
133 <option value="yes">Yes</option>
134 </param> 134 </param>
135 <when value="yes">
136 </when>
135 <when value="no"> 137 <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)" /> 138 <param format="tabular" name="gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />
139 </when> 139 </when>
140 </conditional> 140 </conditional>
141 141
142 </section> 142 </section>
143 </inputs> 143 </inputs>
144 <outputs> 144 <outputs>
145 <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="RSEM.isoforms.results"> 145 <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="RSEM.isoforms.results">
146 <filter>method['est_method'] == "RSEM"</filter> 146 <filter>method['est_method'] == "RSEM"</filter>
147 </data> 147 </data>
148 <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="RSEM.genes.results"> 148 <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="RSEM.genes.results">
149 <filter>method['est_method'] == "RSEM"</filter> 149 <filter>method['est_method'] == "RSEM"</filter>
150 </data> 150 </data>
151 151
152 <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="results.xprs"> 152 <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="results.xprs">
153 <filter>method['est_method'] == "eXpress"</filter> 153 <filter>method['est_method'] == "eXpress"</filter>
154 </data> 154 </data>
155 <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="results.xprs.genes"> 155 <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="results.xprs.genes">
156 <filter>method['est_method'] == "eXpress"</filter> 156 <filter>method['est_method'] == "eXpress"</filter>
163 <param name="right_input" value="reads.right.fq"/> 163 <param name="right_input" value="reads.right.fq"/>
164 <param name="transcripts" value="raw/Trinity.fasta"/> 164 <param name="transcripts" value="raw/Trinity.fasta"/>
165 <param name="library_type" value="RF"/> 165 <param name="library_type" value="RF"/>
166 <param name="est_method" value="RSEM"/> 166 <param name="est_method" value="RSEM"/>
167 <param name="aln_method" value="bowtie"/> 167 <param name="aln_method" value="bowtie"/>
168 <param name="has_gene_map" value="no"/> 168 <param name="has_gene_map" value="yes"/>
169 <output name="isoforms_counts_rsem"> 169 <output name="isoforms_counts_rsem">
170 <assert_contents> 170 <assert_contents>
171 <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" /> 171 <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
172 <has_n_columns n="8" /> 172 <has_n_columns n="8" />
173 </assert_contents> 173 </assert_contents>
185 <param name="right_input" value="reads.right.fq"/> 185 <param name="right_input" value="reads.right.fq"/>
186 <param name="transcripts" value="raw/Trinity.fasta"/> 186 <param name="transcripts" value="raw/Trinity.fasta"/>
187 <param name="library_type" value="RF"/> 187 <param name="library_type" value="RF"/>
188 <param name="est_method" value="RSEM"/> 188 <param name="est_method" value="RSEM"/>
189 <param name="aln_method" value="bowtie2"/> 189 <param name="aln_method" value="bowtie2"/>
190 <param name="has_gene_map" value="no"/> 190 <param name="has_gene_map" value="yes"/>
191 <output name="isoforms_counts_rsem"> 191 <output name="isoforms_counts_rsem">
192 <assert_contents> 192 <assert_contents>
193 <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" /> 193 <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
194 <has_n_columns n="8" /> 194 <has_n_columns n="8" />
195 </assert_contents> 195 </assert_contents>
207 <param name="right_input" value="reads.right.fq"/> 207 <param name="right_input" value="reads.right.fq"/>
208 <param name="transcripts" value="raw/Trinity.fasta"/> 208 <param name="transcripts" value="raw/Trinity.fasta"/>
209 <param name="library_type" value="RF"/> 209 <param name="library_type" value="RF"/>
210 <param name="est_method" value="eXpress"/> 210 <param name="est_method" value="eXpress"/>
211 <param name="aln_method" value="bowtie"/> 211 <param name="aln_method" value="bowtie"/>
212 <param name="has_gene_map" value="no"/> 212 <param name="has_gene_map" value="yes"/>
213 <output name="isoforms_counts_express"> 213 <output name="isoforms_counts_express">
214 <assert_contents> 214 <assert_contents>
215 <has_line_matching expression=".*&#009;TRINITY_DN2_c3_g1_i1&#009;.*" /> 215 <has_line_matching expression=".*&#009;TRINITY_DN2_c3_g1_i1&#009;.*" />
216 <has_n_columns n="15" /> 216 <has_n_columns n="15" />
217 </assert_contents> 217 </assert_contents>
250 250
251 251
252 .. _Trinity: http://trinityrnaseq.github.io 252 .. _Trinity: http://trinityrnaseq.github.io
253 ]]> 253 ]]>
254 </help> 254 </help>
255 255
256 <citations> 256 <citations>
257 <citation type="doi">doi:10.1038/nbt.1883</citation> 257 <citation type="doi">doi:10.1038/nbt.1883</citation>
258 </citations> 258 </citations>
259 </tool> 259 </tool>
260 260