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comparison make.contigs.xml @ 1:2de7963eb3ba draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:19:45 -0400
parents d9268e6b2ea0
children 4cf175b57289
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0:d9268e6b2ea0 1:2de7963eb3ba
2 <description>Aligns paired forward and reverse fastq files to contigs as fasta and quality</description> 2 <description>Aligns paired forward and reverse fastq files to contigs as fasta and quality</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
9 ## create symlinks to input datasets 10 @SHELL_OPTIONS@
10 ln -s "$ffastq" ffastq.dat && 11
11 ln -s "$rfastq" rfastq.dat && 12 ## Symlinks creation or On the fly creation of a combo file
13 #if $input_type.type == 'list_collection'
14 #for $pair in $input_type.list_paired_collection:
15 echo -e "${pair.name}\t${pair.forward}\t${pair.reverse}" >> combo_fastq.dat &&
16 #end for
17 #elif $input_type.type == 'simple_collection'
18 ln -s '$input_type.paired_collection.forward' ffastq.dat &&
19 ln -s '$input_type.paired_collection.reverse' rfastq.dat &&
20 #else
21 ln -s '$input_type.forward_fastq' ffastq.dat &&
22 ln -s '$input_type.reverse_fastq' rfastq.dat &&
23 #end if
24
12 #if $oligo.add == "yes": 25 #if $oligo.add == "yes":
13 ln -s "$oligo.oligos" oligo.oligos.dat && 26 ln -s '$oligo.oligos' oligo.oligos.dat &&
14 ln -s "$oligo.findex" oligo.findex.dat && 27 ln -s '$oligo.findex' oligo.findex.dat &&
15 ln -s "$oligo.rindex" oligo.rindex.dat && 28 ln -s '$oligo.rindex' oligo.rindex.dat &&
16 #end if 29 #end if
17 30
18 echo 'make.contigs( 31 echo 'make.contigs(
19 ffastq=ffastq.dat, 32 #if $input_type.type == 'list_collection':
20 rfastq=rfastq.dat, 33 file=combo_fastq.dat,
34 #else:
35 ffastq=ffastq.dat,
36 rfastq=rfastq.dat,
37 #end if
21 align=$align, 38 align=$align,
22 #if $oligo.add == "yes": 39 #if $oligo.add == "yes":
23 oligos=oligo.oligos.dat, 40 oligos=oligo.oligos.dat,
24 bdiffs=$oligo.bdiffs, 41 bdiffs=$oligo.bdiffs,
25 pdiffs=$oligo.pdiffs, 42 pdiffs=$oligo.pdiffs,
37 gapextend=$gapextend, 54 gapextend=$gapextend,
38 processors='\${GALAXY_SLOTS:-8}' 55 processors='\${GALAXY_SLOTS:-8}'
39 )' 56 )'
40 | sed 's/ //g' ## mothur trips over whitespace 57 | sed 's/ //g' ## mothur trips over whitespace
41 | mothur 58 | mothur
59 | tee mothur.out.log
42 ]]></command> 60 ]]></command>
43 <inputs> 61 <inputs>
44 <param name="ffastq" type="data" format="fastq" label="ffastq - Forward Fastq Sequence file"/> 62 <conditional name="input_type">
45 <param name="rfastq" type="data" format="fastq" label="rfastq - Reverse Fastq Sequence file"/> 63 <param name="type" type="select" label="Select a way to provide forward and reverse fastq files ?" help="">
64 <option value="regular" selected="true">Two simple fastq files (forward and reverse)</option>
65 <option value="simple_collection">One pair (paired collection)</option>
66 <option value="list_collection">Multiple pairs - Combo mode (list:paired collection)</option>
67 </param>
68 <when value="regular">
69 <param name="forward_fastq" type="data" format="fastq" label="Forward reads"/>
70 <param name="reverse_fastq" type="data" format="fastq" label="Reverse reads"/>
71 </when>
72 <when value="simple_collection">
73 <param name="paired_collection" type="data_collection" format="fastq" collection_type="paired" label="Fastq pair (collection)" help="Dataset collection made from a single pair of fastq files (forward + reverse)"/>
74 </when>
75 <when value="list_collection">
76 <param name="list_paired_collection" type="data_collection" format="fastq" collection_type="list:paired" label="Fastq pairs (collection)" help="Dataset collection made from multiple pairs of fastq files" />
77 </when>
78 </conditional>
46 <param name="align" type="select" label="align - Select a pairwise alignment method" help=""> 79 <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
47 <option value="needleman" selected="true">needleman (default) </option> 80 <option value="needleman" selected="true">needleman (default) </option>
48 <option value="gotoh">gotoh</option> 81 <option value="gotoh">gotoh</option>
49 <option value="kmer">kmer</option> 82 <option value="kmer">kmer</option>
50 </param> 83 </param>
53 <option value="no">no</option> 86 <option value="no">no</option>
54 <option value="yes">yes</option> 87 <option value="yes">yes</option>
55 </param> 88 </param>
56 <when value="no"/> 89 <when value="no"/>
57 <when value="yes"> 90 <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"/> 91 <param name="oligos" type="data" format="mothur.oligos" optional="true" label="oligos - barcodes and primers"
92 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)"/> 93 <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)"/> 94 <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)"/> 95 <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)"/> 96 <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)"/> 97 <param name="rindex" type="data" format="fastq" optional="true" label="revese index file (fastq)"/>
68 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/> 102 <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"/> 103 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
70 </inputs> 104 </inputs>
71 <outputs> 105 <outputs>
72 <expand macro="logfile-output"/> 106 <expand macro="logfile-output"/>
73 <data name="fasta" format="fasta" from_work_dir="ffastq*.trim.*.fasta" label="${tool.name} on ${on_string}: trim.contigs.fasta"/> 107 <data name="fasta" format="fasta" from_work_dir="*fastq.trim.*.fasta" label="${tool.name} on ${on_string}: trim.contigs.fasta"/>
74 <data name="qual" format="qual" from_work_dir="ffastq*.trim.*.qual" label="${tool.name} on ${on_string}: trim.contigs.qual"/> 108 <data name="qual" format="qual" from_work_dir="*fastq*.trim.*.qual" label="${tool.name} on ${on_string}: trim.contigs.qual"/>
75 <data name="scrapfasta" format="fasta" from_work_dir="ffastq*.scrap.*.fasta" label="${tool.name} on ${on_string}: scrap.contigs.fasta"/> 109 <data name="scrapfasta" format="fasta" from_work_dir="*fastq*.scrap.*.fasta" label="${tool.name} on ${on_string}: scrap.contigs.fasta"/>
76 <data name="scrapqual" format="qual" from_work_dir="ffastq*.scrap.*.qual" label="${tool.name} on ${on_string}: scrap.contigs.qual"/> 110 <data name="scrapqual" format="qual" from_work_dir="*fastq*.scrap.*.qual" label="${tool.name} on ${on_string}: scrap.contigs.qual"/>
77 <data name="report" format="txt" from_work_dir="ffastq*.contigs.report" label="${tool.name} on ${on_string}: report"/> 111 <data name="report" format="txt" from_work_dir="*fastq*.contigs.report" label="${tool.name} on ${on_string}: report"/>
112 <data name="group" format="mothur.groups" from_work_dir="*fastq*.groups" label="${tool.name} on ${on_string}: group file">
113 <filter>input_type['type'] == 'list_collection'</filter>
114 </data>
78 </outputs> 115 </outputs>
79 <tests> 116 <tests>
80 <test> 117 <!-- Test with two regular files as input -->
81 <param name="ffastq" value="Mock_S280_L001_R1_001_small.fastq"/> 118 <test>
82 <param name="rfastq" value="Mock_S280_L001_R2_001_small.fastq"/> 119 <conditional name="input_type">
120 <param name="type" value="regular"/>
121 <param name="forward_fastq" value="Mock_S280_L001_R1_001_small.fastq" ftype="fastq"/>
122 <param name="reverse_fastq" value="Mock_S280_L001_R2_001_small.fastq" ftype="fastq"/>
123 </conditional>
83 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/> 124 <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"/> 125 <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"/> 126 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
86 <expand macro="logfile-test"/> 127 <expand macro="logfile-test"/>
87 </test> 128 </test>
88 <test> 129 <!-- Test with a simple paired collection as input -->
89 <param name="ffastq" value="Mock_S280_L001_R1_001_small.fastq"/> 130 <test>
90 <param name="rfastq" value="Mock_S280_L001_R2_001_small.fastq"/> 131 <conditional name="input_type">
132 <param name="type" value="simple_collection"/>
133 <param name="paired_collection">
134 <collection type="paired">
135 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
136 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
137 </collection>
138 </param>
139 </conditional>
140 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
141 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/>
142 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
143 <expand macro="logfile-test"/>
144 </test>
145 <!-- Test with a simple paired collection as input + extra parameters specified -->
146 <test>
147 <conditional name="input_type">
148 <param name="type" value="simple_collection"/>
149 <param name="paired_collection">
150 <collection type="paired">
151 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
152 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
153 </collection>
154 </param>
155 </conditional>
91 <param name="align" value="gotoh"/> 156 <param name="align" value="gotoh"/>
92 <param name="match" value="2"/> 157 <param name="match" value="2"/>
93 <param name="mismatch" value="-2"/> 158 <param name="mismatch" value="-2"/>
94 <param name="gapopen" value="-3"/> 159 <param name="gapopen" value="-3"/>
95 <param name="gapextend" value="-2"/> 160 <param name="gapextend" value="-2"/>
96 <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta"/> 161 <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta"/>
97 <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual"/> 162 <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual"/>
98 <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt"/> 163 <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt"/>
99 <expand macro="logfile-test"/> 164 <expand macro="logfile-test"/>
100 </test> 165 </test>
166 <!-- Test with a list:paired collection as input -->
167 <test>
168 <conditional name="input_type">
169 <param name="type" value="list_collection"/>
170 <param name="list_paired_collection">
171 <collection type="list:paired">
172 <element name="Pair1">
173 <collection type="paired">
174 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
175 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
176 </collection>
177 </element>
178 <element name="Pair2">
179 <collection type="paired">
180 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
181 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
182 </collection>
183 </element>
184 </collection>
185 </param>
186 </conditional>
187 <output name="fasta" md5="dab69a0e36f718b55d8defad26ec469b" ftype="fasta"/>
188 <output name="qual" md5="cdba5409e4f87e3cd093a4e51084d616" ftype="qual"/>
189 <output name="report" md5="80b992abd7e4d6a5e89fa70011ef2384" ftype="txt"/>
190 <output name="group" md5="2be2adb030c4fc001bfac7e1172b40e1" ftype="mothur.groups"/>
191 <expand macro="logfile-test"/>
192 </test>
101 </tests> 193 </tests>
102 <help> 194 <help>
103 <![CDATA[ 195 <![CDATA[
104 196
105 @MOTHUR_OVERVIEW@ 197 @MOTHUR_OVERVIEW@
106 198
107 **Command Documenation** 199 **Command Documentation**
108 200
109 The make.contigs_ command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files. 201 The make.contigs_ command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.
110 202
111 .. _make.contigs: http://www.mothur.org/wiki/Make.contigs 203 .. _make.contigs: https://www.mothur.org/wiki/Make.contigs
112 204
113 v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file. 205 v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file.
114 ]]> 206 ]]>
115 </help> 207 </help>
116 <expand macro="citations"/> 208 <expand macro="citations"/>