Mercurial > repos > iuc > mothur_make_fastq

comparison make.fastq.xml @ 3:a17148e8865a 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 09:12:55 -0500
parents 61b2c4a74b35
children 7c99c22d2334
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2:bb99ebc45afe 3:a17148e8865a
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 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 ln -s "$qfile" qfile.dat && 14 ln -s '$qfile' qfile.dat &&
15 15
16 echo 'make.fastq( 16 echo 'make.fastq(
17 fasta=fasta.dat, 17 fasta=fasta.dat,
18 qfile=qfile.dat 18 qfile=qfile.dat
19 #if $chooseformat.use == "yes": 19 #if $chooseformat.use == "yes":
20 ,format=${chooseformat.format} 20 ,format=${chooseformat.format}
21 #end if 21 #end if
22 )' 22 )'
23 | sed 's/ //g' ## mothur trips over whitespace 23 | sed 's/ //g' ## mothur trips over whitespace
24 | mothur 24 | mothur
25 | tee mothur.out.log 25 | tee mothur.out.log
26 ]]></command> 26 ]]></command>
27 <inputs> 27 <inputs>
28 <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/> 28 <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/>
29 <param name="qfile" type="data" format="qual454,qualillumina,qualsolid,qual" label="qfile - Sequence Quality file"/> 29 <param name="qfile" type="data" format="qual454,qualillumina,qualsolid,qual" label="qfile - Sequence Quality file"/>
30 <conditional name="chooseformat"> 30 <conditional name="chooseformat">
57 </outputs> 57 </outputs>
58 <tests> 58 <tests>
59 <test><!-- test defaults --> 59 <test><!-- test defaults -->
60 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> 60 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
61 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> 61 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
62 <output name="fastq" md5="e77b78321620e300946c23147ad599fd" ftype="fastqsanger"/> 62 <output name="fastq" ftype="fastqsanger">
63 <assert_contents>
64 <expand macro="test-fastq-format"/>
65 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
66 </assert_contents>
67 </output>
63 <expand macro="logfile-test"/> 68 <expand macro="logfile-test"/>
64 </test> 69 </test>
65 <test><!-- test with quality score format conversion --> 70 <test><!-- test with quality score format conversion -->
66 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> 71 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
67 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> 72 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
68 <param name="use" value="yes"/> 73 <param name="use" value="yes"/>
69 <param name="format" value="illumina"/> 74 <param name="format" value="illumina"/>
70 <output name="fastq" md5="c792253da205d4d1c66bc87a2969aa25" ftype="fastqillumina"/> 75 <output name="fastq" ftype="fastqillumina">
76 <assert_contents>
77 <expand macro="test-fastq-format"/>
78 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
79 </assert_contents>
80 </output>
71 <expand macro="logfile-test"/> 81 <expand macro="logfile-test"/>
72 </test> 82 </test>
73 </tests> 83 </tests>
74 <help> 84 <help><![CDATA[
75 <![CDATA[
76 85
77 @MOTHUR_OVERVIEW@ 86 @MOTHUR_OVERVIEW@
78 87
79 **Command Documentation** 88 **Command Documentation**
80 89
81 The fastq.info_ command reads a fasta file and quality file and creates a fastq. 90 The make.fastq_ command reads a fasta file and quality file and creates a fastq.
82 91
83 92
84 .. _fastq.info: https://www.mothur.org/wiki/Make.fastq 93 .. _make.fastq: https://www.mothur.org/wiki/Make.fastq
85 ]]> 94
86 </help> 95 ]]></help>
87 <expand macro="citations"/> 96 <expand macro="citations"/>
88 </tool> 97 </tool>