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comparison make.contigs.xml @ 0:d9268e6b2ea0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:37:19 -0400
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1 <tool profile="16.07" id="mothur_make_contigs" name="Make.contigs" version="@WRAPPER_VERSION@.0">
2 <description>Aligns paired forward and reverse fastq files to contigs as fasta and quality</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$ffastq" ffastq.dat &&
11 ln -s "$rfastq" rfastq.dat &&
12 #if $oligo.add == "yes":
13 ln -s "$oligo.oligos" oligo.oligos.dat &&
14 ln -s "$oligo.findex" oligo.findex.dat &&
15 ln -s "$oligo.rindex" oligo.rindex.dat &&
16 #end if
17
18 echo 'make.contigs(
19 ffastq=ffastq.dat,
20 rfastq=rfastq.dat,
21 align=$align,
22 #if $oligo.add == "yes":
23 oligos=oligo.oligos.dat,
24 bdiffs=$oligo.bdiffs,
25 pdiffs=$oligo.pdiffs,
26 tdiffs=$oligo.tdiffs,
27 #if $oligo.findex:
28 findex=oligo.findex.dat,
29 #end if
30 #if $oligo.rindex:
31 rindex=oligo.rindex.dat,
32 #end if
33 #end if
34 match=$match,
35 mismatch=$mismatch,
36 gapopen=$gapopen,
37 gapextend=$gapextend,
38 processors='\${GALAXY_SLOTS:-8}'
39 )'
40 | sed 's/ //g' ## mothur trips over whitespace
41 | mothur
42 ]]></command>
43 <inputs>
44 <param name="ffastq" type="data" format="fastq" label="ffastq - Forward Fastq Sequence file"/>
45 <param name="rfastq" type="data" format="fastq" label="rfastq - Reverse Fastq Sequence file"/>
46 <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
47 <option value="needleman" selected="true">needleman (default) </option>
48 <option value="gotoh">gotoh</option>
49 <option value="kmer">kmer</option>
50 </param>
51 <conditional name="oligo">
52 <param name="add" type="select" label="Trim with an oligos file?" help="">
53 <option value="no">no</option>
54 <option value="yes">yes</option>
55 </param>
56 <when value="no"/>
57 <when value="yes">
58 <param name="oligos" type="data" format="mothur.oligos" optional="true" label="oligos - barcodes and primers" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot; and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file"/>
59 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
60 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
61 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"/>
62 <param name="findex" type="data" format="fastq" optional="true" label="forward index file (fastq)"/>
63 <param name="rindex" type="data" format="fastq" optional="true" label="revese index file (fastq)"/>
64 </when>
65 </conditional>
66 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
67 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
68 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
69 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
70 </inputs>
71 <outputs>
72 <expand macro="logfile-output"/>
73 <data name="fasta" format="fasta" from_work_dir="ffastq*.trim.*.fasta" label="${tool.name} on ${on_string}: trim.contigs.fasta"/>
74 <data name="qual" format="qual" from_work_dir="ffastq*.trim.*.qual" label="${tool.name} on ${on_string}: trim.contigs.qual"/>
75 <data name="scrapfasta" format="fasta" from_work_dir="ffastq*.scrap.*.fasta" label="${tool.name} on ${on_string}: scrap.contigs.fasta"/>
76 <data name="scrapqual" format="qual" from_work_dir="ffastq*.scrap.*.qual" label="${tool.name} on ${on_string}: scrap.contigs.qual"/>
77 <data name="report" format="txt" from_work_dir="ffastq*.contigs.report" label="${tool.name} on ${on_string}: report"/>
78 </outputs>
79 <tests>
80 <test>
81 <param name="ffastq" value="Mock_S280_L001_R1_001_small.fastq"/>
82 <param name="rfastq" value="Mock_S280_L001_R2_001_small.fastq"/>
83 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
84 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/>
85 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
86 <expand macro="logfile-test"/>
87 </test>
88 <test>
89 <param name="ffastq" value="Mock_S280_L001_R1_001_small.fastq"/>
90 <param name="rfastq" value="Mock_S280_L001_R2_001_small.fastq"/>
91 <param name="align" value="gotoh"/>
92 <param name="match" value="2"/>
93 <param name="mismatch" value="-2"/>
94 <param name="gapopen" value="-3"/>
95 <param name="gapextend" value="-2"/>
96 <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta"/>
97 <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual"/>
98 <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt"/>
99 <expand macro="logfile-test"/>
100 </test>
101 </tests>
102 <help>
103 <![CDATA[
104
105 @MOTHUR_OVERVIEW@
106
107 **Command Documenation**
108
109 The make.contigs_ command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.
110
111 .. _make.contigs: http://www.mothur.org/wiki/Make.contigs
112
113 v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file.
114 ]]>
115 </help>
116 <expand macro="citations"/>
117 </tool>