Mercurial > repos > iuc > mothur_make_contigs

annotate make.contigs.xml @ 1:2de7963eb3ba 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/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:19:45 -0400
parents d9268e6b2ea0
children 4cf175b57289
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
1 <tool profile="16.07" id="mothur_make_contigs" name="Make.contigs" version="@WRAPPER_VERSION@.0">
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
2 <description>Aligns paired forward and reverse fastq files to contigs as fasta and quality</description>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
3 <macros>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
4 <import>macros.xml</import>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
5 </macros>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
7 <expand macro="stdio"/>
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
8 <expand macro="version_command"/>
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
9 <command><![CDATA[
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
10 @SHELL_OPTIONS@
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
11
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
12 ## Symlinks creation or On the fly creation of a combo file
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
13 #if $input_type.type == 'list_collection'
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
14 #for $pair in $input_type.list_paired_collection:
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
15 echo -e "${pair.name}\t${pair.forward}\t${pair.reverse}" >> combo_fastq.dat &&
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
16 #end for
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
17 #elif $input_type.type == 'simple_collection'
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
18 ln -s '$input_type.paired_collection.forward' ffastq.dat &&
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
19 ln -s '$input_type.paired_collection.reverse' rfastq.dat &&
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
20 #else
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
21 ln -s '$input_type.forward_fastq' ffastq.dat &&
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
22 ln -s '$input_type.reverse_fastq' rfastq.dat &&
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
23 #end if
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
24
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
25 #if $oligo.add == "yes":
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
26 ln -s '$oligo.oligos' oligo.oligos.dat &&
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
27 ln -s '$oligo.findex' oligo.findex.dat &&
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
28 ln -s '$oligo.rindex' oligo.rindex.dat &&
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
29 #end if
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
30
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
31 echo 'make.contigs(
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
32 #if $input_type.type == 'list_collection':
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
33 file=combo_fastq.dat,
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
34 #else:
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
35 ffastq=ffastq.dat,
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
36 rfastq=rfastq.dat,
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
37 #end if
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
38 align=$align,
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
39 #if $oligo.add == "yes":
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
40 oligos=oligo.oligos.dat,
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
41 bdiffs=$oligo.bdiffs,
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
42 pdiffs=$oligo.pdiffs,
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
43 tdiffs=$oligo.tdiffs,
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
44 #if $oligo.findex:
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
45 findex=oligo.findex.dat,
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
46 #end if
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
47 #if $oligo.rindex:
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
48 rindex=oligo.rindex.dat,
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
49 #end if
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
50 #end if
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
51 match=$match,
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
52 mismatch=$mismatch,
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
53 gapopen=$gapopen,
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
54 gapextend=$gapextend,
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
55 processors='\${GALAXY_SLOTS:-8}'
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
56 )'
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
57 | sed 's/ //g' ## mothur trips over whitespace
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
58 | mothur
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
59 | tee mothur.out.log
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
60 ]]></command>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
61 <inputs>
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
62 <conditional name="input_type">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
63 <param name="type" type="select" label="Select a way to provide forward and reverse fastq files ?" help="">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
64 <option value="regular" selected="true">Two simple fastq files (forward and reverse)</option>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
65 <option value="simple_collection">One pair (paired collection)</option>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
66 <option value="list_collection">Multiple pairs - Combo mode (list:paired collection)</option>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
67 </param>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
68 <when value="regular">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
69 <param name="forward_fastq" type="data" format="fastq" label="Forward reads"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
70 <param name="reverse_fastq" type="data" format="fastq" label="Reverse reads"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
71 </when>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
72 <when value="simple_collection">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
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)"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
74 </when>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
75 <when value="list_collection">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
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" />
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
77 </when>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
78 </conditional>
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
79 <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
80 <option value="needleman" selected="true">needleman (default) </option>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
81 <option value="gotoh">gotoh</option>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
82 <option value="kmer">kmer</option>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
83 </param>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
84 <conditional name="oligo">
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
85 <param name="add" type="select" label="Trim with an oligos file?" help="">
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
86 <option value="no">no</option>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
87 <option value="yes">yes</option>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
88 </param>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
89 <when value="no"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
90 <when value="yes">
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
91 <param name="oligos" type="data" format="mothur.oligos" optional="true" label="oligos - barcodes and primers"
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
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"/>
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
93 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
94 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
95 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
96 <param name="findex" type="data" format="fastq" optional="true" label="forward index file (fastq)"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
97 <param name="rindex" type="data" format="fastq" optional="true" label="revese index file (fastq)"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
98 </when>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
99 </conditional>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
100 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
101 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
102 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
103 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
104 </inputs>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
105 <outputs>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
106 <expand macro="logfile-output"/>
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
107 <data name="fasta" format="fasta" from_work_dir="*fastq.trim.*.fasta" label="${tool.name} on ${on_string}: trim.contigs.fasta"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
108 <data name="qual" format="qual" from_work_dir="*fastq*.trim.*.qual" label="${tool.name} on ${on_string}: trim.contigs.qual"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
109 <data name="scrapfasta" format="fasta" from_work_dir="*fastq*.scrap.*.fasta" label="${tool.name} on ${on_string}: scrap.contigs.fasta"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
110 <data name="scrapqual" format="qual" from_work_dir="*fastq*.scrap.*.qual" label="${tool.name} on ${on_string}: scrap.contigs.qual"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
111 <data name="report" format="txt" from_work_dir="*fastq*.contigs.report" label="${tool.name} on ${on_string}: report"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
112 <data name="group" format="mothur.groups" from_work_dir="*fastq*.groups" label="${tool.name} on ${on_string}: group file">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
113 <filter>input_type['type'] == 'list_collection'</filter>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
114 </data>
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
115 </outputs>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
116 <tests>
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
117 <!-- Test with two regular files as input -->
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
118 <test>
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
119 <conditional name="input_type">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
120 <param name="type" value="regular"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
121 <param name="forward_fastq" value="Mock_S280_L001_R1_001_small.fastq" ftype="fastq"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
122 <param name="reverse_fastq" value="Mock_S280_L001_R2_001_small.fastq" ftype="fastq"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
123 </conditional>
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
124 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
125 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
126 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
127 <expand macro="logfile-test"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
128 </test>
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
129 <!-- Test with a simple paired collection as input -->
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
130 <test>
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
131 <conditional name="input_type">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
132 <param name="type" value="simple_collection"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
133 <param name="paired_collection">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
134 <collection type="paired">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
135 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
136 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
137 </collection>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
138 </param>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
139 </conditional>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
140 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
141 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
142 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
143 <expand macro="logfile-test"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
144 </test>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
145 <!-- Test with a simple paired collection as input + extra parameters specified -->
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
146 <test>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
147 <conditional name="input_type">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
148 <param name="type" value="simple_collection"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
149 <param name="paired_collection">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
150 <collection type="paired">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
151 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
152 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
153 </collection>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
154 </param>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
155 </conditional>
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
156 <param name="align" value="gotoh"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
157 <param name="match" value="2"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
158 <param name="mismatch" value="-2"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
159 <param name="gapopen" value="-3"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
160 <param name="gapextend" value="-2"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
161 <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
162 <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
163 <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
164 <expand macro="logfile-test"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
165 </test>
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
166 <!-- Test with a list:paired collection as input -->
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
167 <test>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
168 <conditional name="input_type">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
169 <param name="type" value="list_collection"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
170 <param name="list_paired_collection">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
171 <collection type="list:paired">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
172 <element name="Pair1">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
173 <collection type="paired">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
174 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
175 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
176 </collection>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
177 </element>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
178 <element name="Pair2">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
179 <collection type="paired">
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
180 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
181 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
182 </collection>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
183 </element>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
184 </collection>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
185 </param>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
186 </conditional>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
187 <output name="fasta" md5="dab69a0e36f718b55d8defad26ec469b" ftype="fasta"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
188 <output name="qual" md5="cdba5409e4f87e3cd093a4e51084d616" ftype="qual"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
189 <output name="report" md5="80b992abd7e4d6a5e89fa70011ef2384" ftype="txt"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
190 <output name="group" md5="2be2adb030c4fc001bfac7e1172b40e1" ftype="mothur.groups"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
191 <expand macro="logfile-test"/>
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
192 </test>
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
193 </tests>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
194 <help>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
195 <![CDATA[
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
196
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
197 @MOTHUR_OVERVIEW@
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
198
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
199 **Command Documentation**
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
200
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
201 The make.contigs_ command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
202
1
2de7963eb3ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
iuc
parents: 0
diff changeset
203 .. _make.contigs: https://www.mothur.org/wiki/Make.contigs
0
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
204
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
205 v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file.
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
206 ]]>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
207 </help>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
208 <expand macro="citations"/>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
209 </tool>