Mercurial > repos > iuc > mothur_make_contigs

comparison make.contigs.xml @ 3:0f563b96b60d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:54:16 -0500
parents 4cf175b57289
children b1b4240133f5
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2:4cf175b57289 3:0f563b96b60d
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"/>
106 </inputs> 110 </inputs>
107 <outputs> 111 <outputs>
108 <expand macro="logfile-output"/> 112 <expand macro="logfile-output"/>
109 <data name="fasta" format="fasta" from_work_dir="*fastq.trim.*.fasta" label="${tool.name} on ${on_string}: trim.contigs.fasta"/> 113 <data name="fasta" format="fasta" from_work_dir="*fastq.trim.*.fasta" label="${tool.name} on ${on_string}: trim.contigs.fasta"/>
110 <data name="qual" format="qual" from_work_dir="*fastq*.trim.*.qual" label="${tool.name} on ${on_string}: trim.contigs.qual"/> 114 <data name="qual" format="qual" from_work_dir="*fastq*.trim.*.qual" label="${tool.name} on ${on_string}: trim.contigs.qual"/>
191 <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/> 195 <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/>
192 <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/> 196 <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/>
193 <expand macro="logfile-test"/> 197 <expand macro="logfile-test"/>
194 </test> 198 </test>
195 </tests> 199 </tests>
196 <help> 200 <help><![CDATA[
197 <![CDATA[
198 201
199 @MOTHUR_OVERVIEW@ 202 @MOTHUR_OVERVIEW@
200 203
201 **Command Documentation** 204 **Command Documentation**
202 205
203 The make.contigs_ command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files. 206 The make.contigs_ command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.
204 207
205 .. _make.contigs: https://www.mothur.org/wiki/Make.contigs 208 .. _make.contigs: https://www.mothur.org/wiki/Make.contigs
206 209
207 v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file. 210 v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file.
208 ]]> 211
209 </help> 212 ]]></help>
210 <expand macro="citations"/> 213 <expand macro="citations"/>
211 </tool> 214 </tool>