Mercurial > repos > devteam > velvet

comparison velvetg.xml @ 1:5da9a0e2fb2d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 8301d37348be25a038b3c63b049b1178d05f5003"
author devteam
date Wed, 12 Feb 2020 11:16:32 -0500
parents 08256557922f
children 8d09f8be269e
comparison
equal deleted inserted replaced
0:08256557922f 1:5da9a0e2fb2d
1 <tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.0"> 1 <tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.1">
2 <description>Velvet sequence assembler for very short reads</description> 2 <description>Velvet sequence assembler for very short reads</description>
3 <version_command>velvetg 2&gt;&amp;1 | grep "Version" | sed -e 's/Version //'</version_command>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
7 <expand macro="requirements"/> 6 <expand macro="requirements"/>
8 <expand macro="stdio"/> 7 <expand macro="stdio"/>
9 <command interpreter="python"> 8 <version_command><![CDATA[
10 velvetg_wrapper.py 9 velvetg 2>&1 | grep "Version" | sed -e 's/Version //'
11 '$input.extra_files_path' 10 ]]></version_command>
12 #if $generate_amos.afg == "yes": 11 <command><![CDATA[
13 -amos_file $generate_amos.afg 12 ln -s '$input.extra_files_path'/Roadmaps &&
14 #end if 13 ln -s '$input.extra_files_path'/Sequences &&
15 #if $unused_reads.generate_unused == "yes": 14 velvetg .
16 -unused_reads $unused_reads.generate_unused 15 #if $generate_amos.afg == "yes":
17 #end if 16 -amos_file $generate_amos.afg
18 $read_trkg 17 #end if
19 #if $coverage.cutoff == "auto": 18 #if $unused_reads.generate_unused == "yes":
20 -cov_cutoff auto 19 -unused_reads $unused_reads.generate_unused
21 #elif $coverage.cutoff == "value": 20 #end if
22 -cov_cutoff $coverage.cov_cutoff 21 $read_trkg
23 #end if 22 #if $coverage.cutoff == "auto":
24 #if $expected.coverage == "auto": 23 -cov_cutoff auto
25 -exp_cov auto 24 #elif $coverage.cutoff == "value":
26 #elif $expected.coverage == "value": 25 -cov_cutoff $coverage.cov_cutoff
27 -exp_cov $expected.exp_cov 26 #end if
28 #end if 27 #if $expected.coverage == "auto":
29 #if $contig_lgth.use_contig_lgth == "yes": 28 -exp_cov auto
30 -min_contig_lgth $contig_lgth.min_contig_lgth 29 #elif $expected.coverage == "value":
31 #end if 30 -exp_cov $expected.exp_cov
32 #if $reads.paired == "yes": 31 #end if
33 #if int($reads.ins_length) > 0: 32 #if $contig_lgth.use_contig_lgth == "yes":
34 -ins_length $reads.ins_length 33 -min_contig_lgth $contig_lgth.min_contig_lgth
35 #end if 34 #end if
36 #if $reads.options.advanced == "yes": 35 #if $reads.paired == "yes":
37 #if int($reads.options.ins_length_sd) > 0: 36 #if int($reads.ins_length) > 0:
38 -ins_length_sd $reads.options.ins_length_sd 37 -ins_length $reads.ins_length
39 #end if 38 #end if
40 #if int($reads.options.ins_length2) > 0: 39 #if $reads.options.advanced == "yes":
41 -ins_length2 $reads.options.ins_length2 40 #if int($reads.options.ins_length_sd) > 0:
42 #end if 41 -ins_length_sd $reads.options.ins_length_sd
43 #if int($reads.options.ins_length2_sd) > 0: 42 #end if
44 -ins_length2_sd $reads.options.ins_length2_sd 43 #if int($reads.options.ins_length2) > 0:
45 #end if 44 -ins_length2 $reads.options.ins_length2
46 #if int($reads.options.ins_length_long) > 0: 45 #end if
47 -ins_length_long $reads.options.ins_length_long 46 #if int($reads.options.ins_length2_sd) > 0:
48 #end if 47 -ins_length2_sd $reads.options.ins_length2_sd
49 #if int($reads.options.ins_length_long_sd) > 0: 48 #end if
50 -ins_length_long_sd $reads.options.ins_length_long_sd 49 #if int($reads.options.ins_length_long) > 0:
51 #end if 50 -ins_length_long $reads.options.ins_length_long
52 #if int($reads.options.max_branch_length) > 0: 51 #end if
53 -max_branch_length $reads.options.max_branch_length 52 #if int($reads.options.ins_length_long_sd) > 0:
54 #end if 53 -ins_length_long_sd $reads.options.ins_length_long_sd
55 #if int($reads.options.max_divergence) > 0: 54 #end if
56 -max_divergence $reads.options.max_divergence 55 #if int($reads.options.max_branch_length) > 0:
57 #end if 56 -max_branch_length $reads.options.max_branch_length
58 #if int($reads.options.max_gap_count) > 0: 57 #end if
59 -max_gap_count $reads.options.max_gap_count 58 #if int($reads.options.max_divergence) > 0:
60 #end if 59 -max_divergence $reads.options.max_divergence
61 #if int($reads.options.min_pair_count) > 0: 60 #end if
62 -min_pair_count $reads.options.min_pair_count 61 #if int($reads.options.max_gap_count) > 0:
63 #end if 62 -max_gap_count $reads.options.max_gap_count
64 #if int($reads.options.max_coverage) > 0: 63 #end if
65 -max_coverage $reads.options.max_coverage 64 #if int($reads.options.min_pair_count) > 0:
66 #end if 65 -min_pair_count $reads.options.min_pair_count
67 #if int($reads.options.long_mult_cutoff) > 0: 66 #end if
68 -long_mult_cutoff $reads.options.long_mult_cutoff 67 #if int($reads.options.max_coverage) > 0:
69 #end if 68 -max_coverage $reads.options.max_coverage
70 $reads.options.scaffolding 69 #end if
71 #end if 70 #if int($reads.options.long_mult_cutoff) > 0:
72 #end if 71 -long_mult_cutoff $reads.options.long_mult_cutoff
73 </command> 72 #end if
73 $reads.options.scaffolding
74 #end if
75 #end if
76 ]]></command>
74 <inputs> 77 <inputs>
75 <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/> 78 <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
76 <conditional name="generate_amos"> 79 <conditional name="generate_amos">
77 <param name="afg" type="select" label="Generate a AMOS.afg file"> 80 <param name="afg" type="select" label="Generate a AMOS.afg file">
78 <option value="no">No</option> 81 <option value="no">No</option>
140 </conditional> 143 </conditional>
141 144
142 <conditional name="reads"> 145 <conditional name="reads">
143 <param name="paired" type="select" label="Using Paired Reads"> 146 <param name="paired" type="select" label="Using Paired Reads">
144 <option value="no">No</option> 147 <option value="no">No</option>
145 <option value="yes" selected="${input.metadata.paired_end_reads}">Yes</option> 148 <option value="yes">Yes</option>
146 </param> 149 </param>
147 <when value="no"/> 150 <when value="no"/>
148 <when value="yes"> 151 <when value="yes">
149 <param name="ins_length" value="-1" label="Insert Length in Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads"/> 152 <param name="ins_length" value="-1" label="Insert Length in Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads"/>
150 <conditional name="options"> 153 <conditional name="options">
186 <filter>unused_reads['generate_unused'] == "yes"</filter> 189 <filter>unused_reads['generate_unused'] == "yes"</filter>
187 </data> 190 </data>
188 <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats" from_work_dir="stats.txt" /> 191 <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats" from_work_dir="stats.txt" />
189 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="contigs.fa" /> 192 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="contigs.fa" />
190 </outputs> 193 </outputs>
191 <requirements>
192 <requirement type="package">velvet</requirement>
193 </requirements>
194 <tests> 194 <tests>
195 <test> 195 <test>
196 <param name="input" value="velveth_test1/output.html" ftype="velvet" > 196 <param name="input" value="velveth_test1/output.html" ftype="velvet">
197 <composite_data value='velveth_test1/Sequences' ftype="Sequences"/> 197 <composite_data value="velveth_test1/Sequences" />
198 <composite_data value='velveth_test1/Roadmaps' ftype="Roadmaps"/> 198 <composite_data value="velveth_test1/Roadmaps" />
199 <composite_data value='velveth_test1/Log'/> 199 <composite_data value="velveth_test1/Log"/>
200 </param> 200 </param>
201 <param name="afg" value="yes" /> 201 <param name="afg" value="yes" />
202 <param name="generate_unused" value="yes" /> 202 <param name="generate_unused" value="yes" />
203 <param name="generate_graph" value="no" /> 203 <param name="generate_graph" value="no" />
204 <param name="read_trkg" value="-read_trkg no" /> 204 <param name="read_trkg" value="-read_trkg no" />
205 <param name="cutoff" value="auto" /> 205 <param name="cutoff" value="auto" />
206 <param name="coverage" value="auto" /> 206 <param name="coverage" value="auto" />
207 <param name="use_contig_lgth" value="no" /> 207 <param name="use_contig_lgth" value="no" />
208 <param name="paired" value="no" /> 208 <param name="paired" value="no" />
209 <!-- 209 <!--
210 <output name="LastGraph" file="velvetg_test1/lastgraph.txt" compare="diff"/> 210 <output name="LastGraph" file="velvetg_test1/lastgraph.txt"/>
211 --> 211 -->
212 <output name="velvet_asm" file="velvetg_test1/amos.afg" compare="diff"/> 212 <output name="velvet_asm" file="velvetg_test1/amos.afg" />
213 <output name="unused_reads_fasta" file="velvetg_test1/unusedreads.fa" compare="diff"/> 213 <output name="unused_reads_fasta" file="velvetg_test1/unusedreads.fa" />
214 <output name="stats" file="velvetg_test1/stats.csv" compare="diff"/> 214 <output name="stats" file="velvetg_test1/stats.csv" />
215 <output name="contigs" file="velvetg_test1/contigs.fa" compare="diff"/> 215 <output name="contigs" file="velvetg_test1/contigs.fa" />
216 </test> 216 </test>
217 </tests> 217 </tests>
218 <help> 218 <help><![CDATA[
219 **What it does** 219 **What it does**
220 220
221 Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. 221 Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
222 222
223 Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs. 223 Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
300 directory/contigs.fa : fasta file of contigs longer than twice hash length 300 directory/contigs.fa : fasta file of contigs longer than twice hash length
301 directory/stats.txt : stats file (tab-spaced) useful for determining appropriate coverage cutoff 301 directory/stats.txt : stats file (tab-spaced) useful for determining appropriate coverage cutoff
302 directory/LastGraph : special formatted file with all the information on the final graph 302 directory/LastGraph : special formatted file with all the information on the final graph
303 directory/velvet_asm.afg : (if requested) AMOS compatible assembly file 303 directory/velvet_asm.afg : (if requested) AMOS compatible assembly file
304 304
305 </help> 305 ]]></help>
306 <expand macro="citation"/> 306 <expand macro="citation"/>
307 </tool> 307 </tool>