Mercurial > repos > iuc > mothur_make_contigs

comparison make.contigs.xml @ 2:bfe5103b1e8f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:58:09 -0400
parents 3dab7d200c10
children 829bb93d3add
comparison
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1:3dab7d200c10 2:bfe5103b1e8f
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## Symlinks creation or On the fly creation of a combo file 12 ## Symlinks creation or On the fly creation of a combo file
13 #if $input_type.type == 'list_collection' 13 #if $input_type.type == 'list_collection'
14 #for $pair in $input_type.list_paired_collection: 14 #for $pair in $input_type.list_paired_collection:
15 ln -s ${pair.forward} `basename ${pair.forward}` && 15 ln -s ${pair.forward} `basename ${pair.forward}` &&
16 ln -s ${pair.reverse} `basename ${pair.reverse}` && 16 ln -s ${pair.reverse} `basename ${pair.reverse}` &&
17 echo -e "${pair.name}\t`basename ${pair.forward}`\t`basename ${pair.reverse}`" >> combo_fastq.dat && 17 echo -e "${pair.name}\t`basename ${pair.forward}`\t`basename ${pair.reverse}`" >> combo_fastq.dat &&
18 #end for 18 #end for
19 #elif $input_type.type == 'simple_collection' 19 #elif $input_type.type == 'simple_collection'
20 ln -s '$input_type.paired_collection.forward' ffastq.dat && 20 ln -s '$input_type.paired_collection.forward' ffastq.dat &&
21 ln -s '$input_type.paired_collection.reverse' rfastq.dat && 21 ln -s '$input_type.paired_collection.reverse' rfastq.dat &&
22 #else 22 #else
23 ln -s '$input_type.forward_fastq' ffastq.dat && 23 ln -s '$input_type.forward_fastq' ffastq.dat &&
24 ln -s '$input_type.reverse_fastq' rfastq.dat && 24 ln -s '$input_type.reverse_fastq' rfastq.dat &&
25 #end if
26
27 #if $oligo.add == "yes":
28 ln -s '$oligo.oligos' oligo.oligos.dat &&
29 ln -s '$oligo.findex' oligo.findex.dat &&
30 ln -s '$oligo.rindex' oligo.rindex.dat &&
31 #end if
32
33 echo 'make.contigs(
34 #if $input_type.type == 'list_collection':
35 file=combo_fastq.dat,
36 #else:
37 ffastq=ffastq.dat,
38 rfastq=rfastq.dat,
39 #end if
40 align=$align,
41 #if $oligo.add == "yes":
42 oligos=oligo.oligos.dat,
43 bdiffs=$oligo.bdiffs,
44 pdiffs=$oligo.pdiffs,
45 tdiffs=$oligo.tdiffs,
46 #if $oligo.findex:
47 findex=oligo.findex.dat,
25 #end if 48 #end if
26 49 #if $oligo.rindex:
27 #if $oligo.add == "yes": 50 rindex=oligo.rindex.dat,
28 ln -s '$oligo.oligos' oligo.oligos.dat &&
29 ln -s '$oligo.findex' oligo.findex.dat &&
30 ln -s '$oligo.rindex' oligo.rindex.dat &&
31 #end if 51 #end if
32 52 #end if
33 echo 'make.contigs( 53 match=$match,
34 #if $input_type.type == 'list_collection': 54 mismatch=$mismatch,
35 file=combo_fastq.dat, 55 gapopen=$gapopen,
36 #else: 56 gapextend=$gapextend,
37 ffastq=ffastq.dat, 57 rename=$rename
38 rfastq=rfastq.dat, 58 processors='\${GALAXY_SLOTS:-8}'
39 #end if 59 )'
40 align=$align, 60 | sed 's/ //g' ## mothur trips over whitespace
41 #if $oligo.add == "yes": 61 | mothur
42 oligos=oligo.oligos.dat, 62 | tee mothur.out.log
43 bdiffs=$oligo.bdiffs,
44 pdiffs=$oligo.pdiffs,
45 tdiffs=$oligo.tdiffs,
46 #if $oligo.findex:
47 findex=oligo.findex.dat,
48 #end if
49 #if $oligo.rindex:
50 rindex=oligo.rindex.dat,
51 #end if
52 #end if
53 match=$match,
54 mismatch=$mismatch,
55 gapopen=$gapopen,
56 gapextend=$gapextend,
57 processors='\${GALAXY_SLOTS:-8}'
58 )'
59 | sed 's/ //g' ## mothur trips over whitespace
60 | mothur
61 | tee mothur.out.log
62 ]]></command> 63 ]]></command>
63 <inputs> 64 <inputs>
64 <conditional name="input_type"> 65 <conditional name="input_type">
65 <param name="type" type="select" label="Select a way to provide forward and reverse fastq files ?" help=""> 66 <param name="type" type="select" label="Select a way to provide forward and reverse fastq files ?" help="">
66 <option value="regular" selected="true">Two simple fastq files (forward and reverse)</option> 67 <option value="regular" selected="true">Two simple fastq files (forward and reverse)</option>
101 </conditional> 102 </conditional>
102 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/> 103 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
103 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/> 104 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
104 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/> 105 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
105 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/> 106 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
107 <param name="rename" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Renames sequences"
108 help="reduce file sizes and greatly reduce the size of the column formatted distance matrix downstream.
109 Uses the rename.seqs command to rename which creates a map file so you can revert to original names at any time"/>
110 <expand macro="param-savelog"/>
106 </inputs> 111 </inputs>
107 <outputs> 112 <outputs>
108 <expand macro="logfile-output"/> 113 <expand macro="logfile-output"/>
109 <data name="fasta" format="fasta" from_work_dir="*fastq.trim.*.fasta" label="${tool.name} on ${on_string}: trim.contigs.fasta"/> 114 <data name="fasta" format="fasta" from_work_dir="*fastq.trim.*.fasta" label="${tool.name} on ${on_string}: trim.contigs.fasta"/>
110 <data name="qual" format="qual" from_work_dir="*fastq*.trim.*.qual" label="${tool.name} on ${on_string}: trim.contigs.qual"/> 115 <data name="qual" format="qual" from_work_dir="*fastq*.trim.*.qual" label="${tool.name} on ${on_string}: trim.contigs.qual"/>
124 <param name="reverse_fastq" value="Mock_S280_L001_R2_001_small.fastq" ftype="fastq"/> 129 <param name="reverse_fastq" value="Mock_S280_L001_R2_001_small.fastq" ftype="fastq"/>
125 </conditional> 130 </conditional>
126 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/> 131 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
127 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/> 132 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/>
128 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/> 133 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
134 <param name="savelog" value="true"/>
129 <expand macro="logfile-test"/> 135 <expand macro="logfile-test"/>
130 </test> 136 </test>
131 <!-- Test with a simple paired collection as input --> 137 <!-- Test with a simple paired collection as input -->
132 <test> 138 <test>
133 <conditional name="input_type"> 139 <conditional name="input_type">
140 </param> 146 </param>
141 </conditional> 147 </conditional>
142 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/> 148 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
143 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/> 149 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/>
144 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/> 150 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
151 <param name="savelog" value="true"/>
145 <expand macro="logfile-test"/> 152 <expand macro="logfile-test"/>
146 </test> 153 </test>
147 <!-- Test with a simple paired collection as input + extra parameters specified --> 154 <!-- Test with a simple paired collection as input + extra parameters specified -->
148 <test> 155 <test>
149 <conditional name="input_type"> 156 <conditional name="input_type">
161 <param name="gapopen" value="-3"/> 168 <param name="gapopen" value="-3"/>
162 <param name="gapextend" value="-2"/> 169 <param name="gapextend" value="-2"/>
163 <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta"/> 170 <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta"/>
164 <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual"/> 171 <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual"/>
165 <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt"/> 172 <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt"/>
173 <param name="savelog" value="true"/>
166 <expand macro="logfile-test"/> 174 <expand macro="logfile-test"/>
167 </test> 175 </test>
168 <!-- Test with a list:paired collection as input --> 176 <!-- Test with a list:paired collection as input -->
169 <test> 177 <test>
170 <conditional name="input_type"> 178 <conditional name="input_type">
188 </conditional> 196 </conditional>
189 <output name="fasta" md5="91bd3b91adc6559182ad118b767f0a07" ftype="fasta"/> 197 <output name="fasta" md5="91bd3b91adc6559182ad118b767f0a07" ftype="fasta"/>
190 <output name="qual" md5="7094d1ac82a40e9f89cc6cdf5e214da7" ftype="qual"/> 198 <output name="qual" md5="7094d1ac82a40e9f89cc6cdf5e214da7" ftype="qual"/>
191 <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/> 199 <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/>
192 <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/> 200 <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/>
201 <param name="savelog" value="true"/>
193 <expand macro="logfile-test"/> 202 <expand macro="logfile-test"/>
194 </test> 203 </test>
195 </tests> 204 </tests>
196 <help> 205 <help><![CDATA[
197 <![CDATA[
198 206
199 @MOTHUR_OVERVIEW@ 207 @MOTHUR_OVERVIEW@
200 208
201 **Command Documentation** 209 **Command Documentation**
202 210
203 The make.contigs_ command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files. 211 The make.contigs_ command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.
204 212
205 .. _make.contigs: https://www.mothur.org/wiki/Make.contigs 213 .. _make.contigs: https://www.mothur.org/wiki/Make.contigs
206 214
207 v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file. 215 v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file.
208 ]]> 216
209 </help> 217 ]]></help>
210 <expand macro="citations"/> 218 <expand macro="citations"/>
211 </tool> 219 </tool>