Mercurial > repos > iuc > shovill

annotate shovill.xml @ 4:d9f6a00b6db7 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-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
author iuc
date Sun, 25 Aug 2019 05:14:31 -0400
parents 865119fcb694
children 8d1af5db538d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
1 <tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy0">
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
2 <description>Faster SPAdes assembly of Illumina reads</description>
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
3 <macros>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
4 <token name="@TOOL_VERSION@">1.0.4</token>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
5 </macros>
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
6 <requirements>
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">shovill</requirement>
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
8 </requirements>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
9 <version_command>shovill --version</version_command>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
11 #if str($library.lib_type) == "paired"
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
12 #set r1_ext = $library.R1.extension
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
13 #set r2_ext = $library.R2.extension
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
14 ln -s '$library.R1' fastq_r1.'$r1_ext' &&
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
15 ln -s '$library.R2' fastq_r2.'$r2_ext' &&
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
16 #else if str($library.lib_type) == "collection"
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
17 #set r1_ext = $library.input1.forward.extension
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
18 #set r2_ext = $library.input1.reverse.extension
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
19 ln -s '$library.input1.forward' fastq_r1.'$r1_ext' &&
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
20 ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' &&
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
21 #end if
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
22
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
23 shovill
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
24 --outdir 'out'
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
25 --cpus \${GALAXY_SLOTS:-1}
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
26 --ram \${SHOVILL_RAM:-4}
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
27 --R1 fastq_r1.'$r1_ext'
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
28 --R2 fastq_r2.'$r2_ext'
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
29 $trim
2
f698c7604b3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
30 --namefmt '$adv.namefmt'
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
31 --depth '$adv.depth'
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
32 #if $adv.gsize
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
33 --gsize '$adv.gsize'
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
34 #end if
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
35 #if $adv.kmers
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
36 --kmers '$adv.kmers'
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
37 #end if
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
38 #if $adv.opts
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
39 --opts '$adv.opts'
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
40 #end if
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
41 $adv.nocorr
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
42 --minlen $adv.minlen
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
43 --mincov $adv.mincov
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
44 --assembler $assembler
1
57d5928f456e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents: 0
diff changeset
45
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
46 ]]></command>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
47 <inputs>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
48 <conditional name="library">
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
49 <param name="lib_type" type="select" label="Input reads type, collection or single library" help="Select 'paired end' for a single library or 'collection' for a paired end collection">
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
50 <option value="paired" selected="true">Paired End</option>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
51 <option value="collection">Paired Collection</option>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
52 </param>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
53 <when value="paired">
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
54 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
55 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
56 </when>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
57 <when value="collection">
1
57d5928f456e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents: 0
diff changeset
58 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
59 </when>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
60 </conditional>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
61 <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
62 <param name="log" type="boolean" label="Output log file?" checked="true" help="Return the Shovill log file as part of the output. Default is on" />
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
63 <param name="assembler" argument="--assembler" type="select" label="Assembler to use" help="Which assembler would you like shovill to use, default is Spades">
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
64 <option value="skesa">skesa</option>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
65 <option value="megahit">megahit</option>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
66 <option value="velvet">velvet</option>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
67 <option value="spades" selected="true">Spades</option>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
68 </param>
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
69 <section name="adv" title="Advanced options" expanded="False">
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
70 <param name="namefmt" argument="--namefmt" type="text" value="contig%05d" label="Contig name format" help="Format of contig FASTA IDs in 'printf' style (default: 'contig%05d')" >
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
71 <sanitizer>
2
f698c7604b3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
72 <valid initial="string.printable">
f698c7604b3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
73 <remove value="&apos;" />
f698c7604b3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
74 </valid>
f698c7604b3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
75 <mapping initial="none">
f698c7604b3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
76 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
f698c7604b3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
77 </mapping>
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
78 </sanitizer>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
79 </param>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
80 <param name="depth" argument="--depth" type="integer" value="100" label="Depth" help="Sub-sample --R1/--R2 to this depth. Disable with --depth 0 (default: 100)" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
81 <param name="gsize" argument="--gsize" type="text" value="" label="Estimated genome size" help="An estimate of the final genome size, it will autodetect if this is blank. (default: '')" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
82 <param name="kmers" argument="--kmers" type="text" value="" label="List of kmer sizes to use" help="List of K-mer sizes to use in SPAdes. Blank is AUTO. default: ''" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
83 <param name="opts" argument="--opts" type="text" value="" label="Extra SPAdes options" help="eg. --plasmid --sc ... (default: '')" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
84 <param name="nocorr" argument="--nocorr" type="boolean" truevalue="--nocorr" falsevalue="" checked="True" label="Disable post-assembly correction" help="Disable post assembly correction with pilon (default: ON)" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
85 <param name="minlen" argument="--minlen" type="integer" value="0" label="Minimum contig length" help="Minimum length of contig to be output. 0 is AUTO (default: 0)" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
86 <param name="mincov" argument="--mincov" type="integer" value="2" label="Minimum contig coverage" help="Minimum coverage to call part of a contig. 0 is AUTO (default: 2)" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
87 </section>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
88 </inputs>
1
57d5928f456e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents: 0
diff changeset
89
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
90 <outputs>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
91 <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/shovill.log" >
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
92 <filter>log</filter>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
93 </data>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
94 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
95 <data format="txt" name="contigs_graph" label="${tool.name} on ${on_string}: Contig Graph" from_work_dir="out/contigs.gfa"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
96 </outputs>
1
57d5928f456e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents: 0
diff changeset
97
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
98 <tests>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
99 <test> <!-- Test 1: Basic test -->
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
100 <param name="lib_type" value="paired" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
101 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
102 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
103 <output name="contigs" ftype="fasta">
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
104 <assert_contents>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
105 <has_text text="&gt;contig00001"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
106 </assert_contents>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
107 </output>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
108 <output name="shovill_std_log" ftype="txt" >
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
109 <assert_contents>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
110 <has_text text="[mash]"/>
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
111 <has_text text="[lighter] Processed 1714 reads"/>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
112 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
113 <has_text text="[spades] ======= SPAdes pipeline finished."/>
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
114 </assert_contents>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
115 </output>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
116 </test>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
117 <test> <!-- Test 2: Auto everything + trim + different name format test -->
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
118 <param name="lib_type" value="paired" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
119 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
120 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
121 <param name="trim" value="true" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
122 <section name="adv">
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
123 <param name="depth" value="0"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
124 <param name="minlen" value="0"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
125 <param name="mincov" value="0"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
126 <param name="nocorr" value="false"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
127 <param name="namefmt" value="contig%03d"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
128 </section>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
129 <output name="contigs" ftype="fasta">
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
130 <assert_contents>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
131 <has_text text="&gt;contig001"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
132 </assert_contents>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
133 </output>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
134 <output name="shovill_std_log" ftype="txt" >
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
135 <assert_contents>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
136 <has_text text="[mash] Writing to"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
137 <has_text text="[trimmomatic] TrimmomaticPE: Completed successfully"/>
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
138 <has_text text="[lighter] Processed 2000 reads:"/>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
139 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
140 <has_text text="[spades] ======= SPAdes pipeline finished."/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
141 <has_text text="[bwa+samtools-sort] [samclip] Done."/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
142 <has_text text="[pilon] Mean total coverage:"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
143 <has_text text="[shovill] Done."/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
144 </assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
145 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
146 </test>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
147 <test> <!-- Test 3: Alternate assembler #1: Megahit -->
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
148 <param name="lib_type" value="paired" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
149 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
150 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
151 <param name="assembler" value="megahit" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
152 <output name="contigs" ftype="fasta">
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
153 <assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
154 <has_text text="&gt;contig00001"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
155 </assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
156 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
157 <output name="shovill_std_log" ftype="txt" >
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
158 <assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
159 <has_text text="[mash]"/>
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
160 <has_text text="[lighter] Processed 1714 reads"/>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
161 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
162 <has_text_matching expression="\[megahit\] .* ALL DONE"/>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
163 </assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
164 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
165 </test>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
166 <test> <!-- Test 4: Alternate assembler #2: Skesa -->
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
167 <param name="lib_type" value="paired" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
168 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
169 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
170 <param name="assembler" value="skesa" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
171 <output name="contigs" ftype="fasta">
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
172 <assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
173 <has_text text="&gt;contig00001"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
174 </assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
175 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
176 <output name="shovill_std_log" ftype="txt" >
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
177 <assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
178 <has_text text="[mash]"/>
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
179 <has_text text="[lighter] Processed 1714 reads"/>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
180 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
181 <has_text text="[skesa] DONE"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
182 </assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
183 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
184 </test>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
185 <test> <!-- Test 5: Alternate assembler #3: Velvet -->
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
186 <param name="lib_type" value="paired" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
187 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
188 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
189 <param name="assembler" value="velvet" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
190 <output name="contigs" ftype="fasta">
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
191 <assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
192 <has_text text="&gt;contig00001"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
193 </assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
194 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
195 <output name="shovill_std_log" ftype="txt" >
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
196 <assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
197 <has_text text="[mash]"/>
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
198 <has_text text="[lighter] Processed 1714 reads"/>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
199 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
200 <has_text text="[velvetg] Final graph has"/>
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
201 </assert_contents>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
202 </output>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
203 </test>
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
204 <test> <!-- Test 6: Gzipped input with trimming -->
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
205 <param name="lib_type" value="paired" />
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
206 <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger" />
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
207 <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger" />
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
208 <param name="trim" value="true" />
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
209 <output name="contigs" ftype="fasta">
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
210 <assert_contents>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
211 <has_text text="&gt;contig00001"/>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
212 </assert_contents>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
213 </output>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
214 <output name="shovill_std_log" ftype="txt" >
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
215 <assert_contents>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
216 <has_text text="[mash]"/>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
217 <has_text text="[lighter] Processed 1714 reads"/>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
218 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
219 <has_text text="[spades] ======= SPAdes pipeline finished."/>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
220 </assert_contents>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
221 </output>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
222 </test>
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
223 </tests>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
224 <help><![CDATA[
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
225 Synopsis:
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
226 Faster de novo assembly pipeline for Illumina paired end reads based around Spades
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
227
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
228 Details and options:
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
229 - Takes paired end Illumina fastq reads
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
230 - Trim reads: Use Trimmomatic to remove common adaptors first (default: OFF)
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
231 - Output log file: If set to "Yes", tool will return Shovill's log file as part of the output
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
232 - Assembler: Which assembler should shovill use from: Skesa, Megahit, Velvet or Spades. Spades is the default.
1
57d5928f456e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents: 0
diff changeset
233
57d5928f456e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents: 0
diff changeset
234 Advanced options:
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
235 - Name format: Format of output contig FASTA IDs in 'printf' style (default: 'contig%05d')
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
236 - Depth: Sub-sample the reads to this depth. Disable with *Depth: 0* (default: 100)
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
237 - Estimated genomesize: An estimate of the final genome size, it will autodetect if this is blank. (default: '')
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
238 - List of kmers to use: List of K-mer sizes to use in SPAdes. Blank is AUTO. (default: '')
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
239 - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: '')
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
240 - Disable post-assembly correction: Disable post assembly correction with pilon (default: ON)
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
241 - Minimum contig length: Minimum length of contig to be output. 0 is AUTO (default: 0)
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
242 - Minimum contig coverage: Minimum coverage to call part of a contig. 0 is AUTO (default: 2)
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
243 - Spades result to correct: Spades result to correct: before_rr, contigs or scaffolds (default: 'contigs')
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
244
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
245 Documentation can be found at Torsten Seemann `site <https://github.com/tseemann/shovill>`_.
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
246 ]]></help>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
247 <citations>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
248 <citation type="bibtex">
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
249 @UNPUBLISHED{Seemann2017,
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
250 author = {Seemann, Torsten},
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
251 title = {Shovill: Faster SPAdes assembly of Illumina reads},
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
252 year = {2017},
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
253 url = {https://github.com/tseemann/shovill},
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
254 }
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
255 </citation>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
256 </citations>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
257 </tool>