comparison fastq.info.xml @ 0:19316e7c4802 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:29:45 -0400
parents
children 1aa945e00ef2
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-1:000000000000 0:19316e7c4802
1 <tool profile="16.07" id="mothur_fastq_info" name="Fastq.info" version="@WRAPPER_VERSION@.0">
2 <description>Convert fastq to fasta and quality</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$fastq" fastq.dat &&
14 #if $oligo.add == "yes":
15 ln -s "$oligo.oligos" oligo.oligos.dat &&
16 #end if
17
18 echo 'fastq.info(
19 fastq=fastq.dat,
20 pacbio=$pacbio,
21 format=$format
22 #if $oligo.add == "yes":
23 ,oligos=oligo.oligos.dat
24 ,bdiffs=$oligo.bdiffs
25 ,pdiffs=$oligo.pdiffs
26 ,tdiffs=$oligo.tdiffs
27 ,ldiffs=$oligo.ldiffs
28 ,sdiffs=$oligo.sdiffs
29 #end if
30 )'
31 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur
33 | tee mothur.out.log
34 ## rename some outputs
35 #if $oligo.add == "yes":
36 && mv fastq.scrap.fasta scrap.fasta
37 && mv fastq.scrap.qual scrap.qual
38 #end if
39 ]]></command>
40 <inputs>
41 <param name="fastq" type="data" format="fastq" label="fastq - Fastq Sequence file"/>
42 <param name="pacbio" type="boolean" truevalue="true" falsevalue="false" checked="false" label="pacbio - if set to true, quality scores of 0 will results in a corresponding base of N"/>
43 <param name="format" type="select" label="format of sequence">
44 <option value="sanger" selected="true">sanger</option>
45 <option value="solexa">solexa</option>
46 <option value="illumina">illumina</option>
47 <option value="illumina1.8+">illumina1.8+</option>
48 </param>
49 <conditional name="oligo">
50 <param name="add" type="select" label="Use oligos file?" help="a file that 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.">
51 <option value="no">no</option>
52 <option value="yes">yes</option>
53 </param>
54 <when value="yes">
55 <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/>
56 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (must be > 0; default 0)"/>
57 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (must be > 0; default 0)"/>
58 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (must be > 0; default 0)"/>
59 <param name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (must be > 0; default 0)"/>
60 <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (must be > 0; default 0)"/>
61 </when>
62 <when value="no"/>
63 </conditional>
64 </inputs>
65 <outputs>
66 <expand macro="logfile-output"/>
67 <data name="fasta_out" format="fasta" from_work_dir="fastq*.fasta" label="${tool.name} on ${on_string}: fasta"/>
68 <data name="qfile_out" format="qual454" from_work_dir="fastq*.qual" label="${tool.name} on ${on_string}: qual"/>
69 <data name="fastq_scrap_out" format="fastq" from_work_dir="fastq*.scrap.fastq" label="${tool.name} on ${on_string}: fastq scrap">
70 <filter>oligos</filter>
71 </data>
72 <data name="fasta_scrap_out" format="fasta" from_work_dir="scrap.fasta" label="${tool.name} on ${on_string}: fasta scrap">
73 <filter>oligos</filter>
74 </data>
75 <data name="qfile_scrap_out" format="qual454" from_work_dir="scrap.qual" label="${tool.name} on ${on_string}: qual scrap">
76 <filter>oligos</filter>
77 </data>
78 </outputs>
79 <tests>
80 <test>
81 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/>
82 <param name="pacbio" value="false"/>
83 <param name="format" value="sanger"/>
84 <param name="add" value="no"/>
85 <output name="fasta_out" md5="88c573d00181be6dd519a0c9599f8b0c"/>
86 <output name="qfile_out" md5="d382c496c583b1501666459757cabbe3"/>
87 <expand macro="logfile-test"/>
88 </test>
89 <test>
90 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/>
91 <param name="pacbio" value="false"/>
92 <param name="format" value="sanger"/>
93 <param name="add" value="yes"/>
94 <param name="oligos" value="GQY1XT001.oligos"/>
95 <param name="bdiffs" value="1"/>
96 <param name="pdiffs" value="3"/>
97 <param name="tdiffs" value="3"/>
98 <param name="ldiffs" value="3"/>
99 <param name="sdiffs" value="7"/>
100 <output name="fasta_out" md5="88c573d00181be6dd519a0c9599f8b0c" ftype="fasta"/>
101 <output name="qfile_out" md5="d382c496c583b1501666459757cabbe3" ftype="qual454"/>
102 <output name="fastq_scrap_out" md5="37a280b8af54af2a0a52b2eba1e58933" ftype="fastq"/>
103 <output name="fasta_scrap_out" md5="88c573d00181be6dd519a0c9599f8b0c" ftype="fasta"/>
104 <output name="qfile_scrap_out" md5="96c2f7ea3cf6336d50bef2c087280c01" ftype="qual454"/>
105 <expand macro="logfile-test"/>
106 </test>
107 <test>
108 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/>
109 <param name="pacbio" value="false"/>
110 <param name="format" value="sanger"/>
111 <param name="add" value="yes"/>
112 <param name="oligos" value="HMPv5-v3_1368-1369.oligos"/>
113 <param name="bdiffs" value="1"/>
114 <param name="pdiffs" value="3"/>
115 <param name="tdiffs" value="3"/>
116 <param name="ldiffs" value="3"/>
117 <param name="sdiffs" value="7"/>
118 <output name="fasta_out" md5="88c573d00181be6dd519a0c9599f8b0c"/>
119 <output name="qfile_out" md5="d382c496c583b1501666459757cabbe3"/>
120 <output name="fastq_scrap_out" md5="37a280b8af54af2a0a52b2eba1e58933"/>
121 <output name="fasta_scrap_out" md5="88c573d00181be6dd519a0c9599f8b0c"/>
122 <output name="qfile_scrap_out" md5="96c2f7ea3cf6336d50bef2c087280c01"/>
123 <expand macro="logfile-test"/>
124 </test>
125 </tests>
126 <help>
127 <![CDATA[
128
129 @MOTHUR_OVERVIEW@
130
131 **Command Documentation**
132
133 The fastq.info_ command reads a fastq file and creates a fasta and quality file.
134
135
136 .. _fastq.info: https://www.mothur.org/wiki/Fastq.info
137 ]]>
138 </help>
139 <expand macro="citations"/>
140 </tool>