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comparison fastq.info.xml @ 2:1aa945e00ef2 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 22:01:25 -0400
parents 19316e7c4802
children 22da6f6c5be8
comparison
equal deleted inserted replaced
1:7332408e1f37 2:1aa945e00ef2
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 "$fastq" fastq.dat && 13 ln -s '$fastq' fastq.dat &&
14 #if $oligo.add == "yes": 14 #if $oligo.add == "yes":
15 ln -s "$oligo.oligos" oligo.oligos.dat && 15 ln -s '$oligo.oligos' oligo.oligos.dat &&
16 #end if 16 #end if
17 17
18 echo 'fastq.info( 18 echo 'fastq.info(
19 fastq=fastq.dat, 19 fastq=fastq.dat,
20 pacbio=$pacbio, 20 pacbio=$pacbio,
21 format=$format 21 format=$format
22 #if $oligo.add == "yes": 22 #if $oligo.add == "yes":
23 ,oligos=oligo.oligos.dat 23 ,oligos=oligo.oligos.dat
24 ,bdiffs=$oligo.bdiffs 24 ,bdiffs=$oligo.bdiffs
25 ,pdiffs=$oligo.pdiffs 25 ,pdiffs=$oligo.pdiffs
26 ,tdiffs=$oligo.tdiffs 26 ,tdiffs=$oligo.tdiffs
27 ,ldiffs=$oligo.ldiffs 27 ,ldiffs=$oligo.ldiffs
28 ,sdiffs=$oligo.sdiffs 28 ,sdiffs=$oligo.sdiffs
29 #end if 29 #end if
30 )' 30 )'
31 | sed 's/ //g' ## mothur trips over whitespace 31 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur 32 | mothur
33 | tee mothur.out.log 33 | tee mothur.out.log
34 ## rename some outputs 34 ## rename some outputs
35 #if $oligo.add == "yes": 35 #if $oligo.add == "yes":
36 && mv fastq.scrap.fasta scrap.fasta 36 && mv fastq.scrap.fasta scrap.fasta
37 && mv fastq.scrap.qual scrap.qual 37 && mv fastq.scrap.qual scrap.qual
38 #end if 38 #end if
39 ]]></command> 39 ]]></command>
40 <inputs> 40 <inputs>
41 <param name="fastq" type="data" format="fastq" label="fastq - Fastq Sequence file"/> 41 <param argument="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"/> 42 <param argument="pacbio" type="boolean" truevalue="true" falsevalue="false" checked="false"
43 <param name="format" type="select" label="format of sequence"> 43 label="pacbio - if set to true, quality scores of 0 will results in a corresponding base of N"/>
44 <param argument="format" type="select" label="format of sequence">
44 <option value="sanger" selected="true">sanger</option> 45 <option value="sanger" selected="true">sanger</option>
45 <option value="solexa">solexa</option> 46 <option value="solexa">solexa</option>
46 <option value="illumina">illumina</option> 47 <option value="illumina">illumina</option>
47 <option value="illumina1.8+">illumina1.8+</option> 48 <option value="illumina1.8+">illumina1.8+</option>
48 </param> 49 </param>
49 <conditional name="oligo"> 50 <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 <param name="add" type="select" label="Use oligos file?"
52 help="a file that contain the sequences of the forward and reverse primers and barcodes and their sample identifier.
53 Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot;
54 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> 55 <option value="no">no</option>
52 <option value="yes">yes</option> 56 <option value="yes">yes</option>
53 </param> 57 </param>
54 <when value="yes"> 58 <when value="yes">
55 <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/> 59 <param argument="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)"/> 60 <param argument="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)"/> 61 <param argument="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)"/> 62 <param argument="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)"/> 63 <param argument="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)"/> 64 <param argument="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> 65 </when>
62 <when value="no"/> 66 <when value="no"/>
63 </conditional> 67 </conditional>
68 <expand macro="param-savelog"/>
64 </inputs> 69 </inputs>
65 <outputs> 70 <outputs>
66 <expand macro="logfile-output"/> 71 <expand macro="logfile-output"/>
67 <data name="fasta_out" format="fasta" from_work_dir="fastq*.fasta" label="${tool.name} on ${on_string}: fasta"/> 72 <data name="fasta_out" format="fasta" from_work_dir="fastq*.fasta" label="${tool.name} on ${on_string}: fasta"/>
68 <data name="qfile_out" format="qual454" from_work_dir="fastq*.qual" label="${tool.name} on ${on_string}: qual"/> 73 <data name="qfile_out" format="qual454" from_work_dir="fastq*.qual" label="${tool.name} on ${on_string}: qual"/>
79 <tests> 84 <tests>
80 <test> 85 <test>
81 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/> 86 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/>
82 <param name="pacbio" value="false"/> 87 <param name="pacbio" value="false"/>
83 <param name="format" value="sanger"/> 88 <param name="format" value="sanger"/>
84 <param name="add" value="no"/> 89 <param name="oligo|add" value="no"/>
85 <output name="fasta_out" md5="88c573d00181be6dd519a0c9599f8b0c"/> 90 <output name="fasta_out" ftype="fasta">
86 <output name="qfile_out" md5="d382c496c583b1501666459757cabbe3"/> 91 <assert_contents>
92 <expand macro="test-fasta-format"/>
93 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
94 </assert_contents>
95 </output>
96 <output name="qfile_out">
97 <assert_contents>
98 <expand macro="test-qfile-format"/>
99 <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>
100 </assert_contents>
101 </output>
102 <param name="savelog" value="true"/>
87 <expand macro="logfile-test"/> 103 <expand macro="logfile-test"/>
88 </test> 104 </test>
89 <test> 105 <test>
90 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/> 106 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/>
91 <param name="pacbio" value="false"/> 107 <param name="pacbio" value="false"/>
92 <param name="format" value="sanger"/> 108 <param name="format" value="sanger"/>
93 <param name="add" value="yes"/> 109 <param name="oligo|add" value="yes"/>
94 <param name="oligos" value="GQY1XT001.oligos"/> 110 <param name="oligos" value="GQY1XT001.oligos"/>
95 <param name="bdiffs" value="1"/> 111 <param name="bdiffs" value="1"/>
96 <param name="pdiffs" value="3"/> 112 <param name="pdiffs" value="3"/>
97 <param name="tdiffs" value="3"/> 113 <param name="tdiffs" value="3"/>
98 <param name="ldiffs" value="3"/> 114 <param name="ldiffs" value="3"/>
99 <param name="sdiffs" value="7"/> 115 <param name="sdiffs" value="7"/>
100 <output name="fasta_out" md5="88c573d00181be6dd519a0c9599f8b0c" ftype="fasta"/> 116 <output name="fasta_out" ftype="fasta">
101 <output name="qfile_out" md5="d382c496c583b1501666459757cabbe3" ftype="qual454"/> 117 <assert_contents>
102 <output name="fastq_scrap_out" md5="37a280b8af54af2a0a52b2eba1e58933" ftype="fastq"/> 118 <expand macro="test-fasta-format"/>
103 <output name="fasta_scrap_out" md5="88c573d00181be6dd519a0c9599f8b0c" ftype="fasta"/> 119 </assert_contents>
104 <output name="qfile_scrap_out" md5="96c2f7ea3cf6336d50bef2c087280c01" ftype="qual454"/> 120 </output>
121 <output name="qfile_out" ftype="qual454">
122 <assert_contents>
123 <expand macro="test-qfile-format"/>
124 <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>
125 </assert_contents>
126 </output>
127 <output name="fastq_scrap_out" ftype="fastq">
128 <assert_contents>
129 <expand macro="test-fastq-format"/>
130 <has_text text="@M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
131 </assert_contents>
132 </output>
133 <output name="fasta_scrap_out" ftype="fasta">
134 <assert_contents>
135 <expand macro="test-fasta-format"/>
136 </assert_contents>
137 </output>
138 <output name="qfile_scrap_out" ftype="qual454">
139 <assert_contents>
140 <expand macro="test-qfile-format"/>
141 <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>
142 </assert_contents>
143 </output>
144 <param name="savelog" value="true"/>
105 <expand macro="logfile-test"/> 145 <expand macro="logfile-test"/>
106 </test> 146 </test>
107 <test> 147 <test>
108 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/> 148 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/>
109 <param name="pacbio" value="false"/> 149 <param name="pacbio" value="false"/>
110 <param name="format" value="sanger"/> 150 <param name="format" value="sanger"/>
111 <param name="add" value="yes"/> 151 <param name="oligo|add" value="yes"/>
112 <param name="oligos" value="HMPv5-v3_1368-1369.oligos"/> 152 <param name="oligos" value="HMPv5-v3_1368-1369.oligos"/>
113 <param name="bdiffs" value="1"/> 153 <param name="bdiffs" value="1"/>
114 <param name="pdiffs" value="3"/> 154 <param name="pdiffs" value="3"/>
115 <param name="tdiffs" value="3"/> 155 <param name="tdiffs" value="3"/>
116 <param name="ldiffs" value="3"/> 156 <param name="ldiffs" value="3"/>
117 <param name="sdiffs" value="7"/> 157 <param name="sdiffs" value="7"/>
118 <output name="fasta_out" md5="88c573d00181be6dd519a0c9599f8b0c"/> 158 <output name="fasta_out">
119 <output name="qfile_out" md5="d382c496c583b1501666459757cabbe3"/> 159 <assert_contents>
120 <output name="fastq_scrap_out" md5="37a280b8af54af2a0a52b2eba1e58933"/> 160 <expand macro="test-fasta-format"/>
121 <output name="fasta_scrap_out" md5="88c573d00181be6dd519a0c9599f8b0c"/> 161 </assert_contents>
122 <output name="qfile_scrap_out" md5="96c2f7ea3cf6336d50bef2c087280c01"/> 162 </output>
163 <output name="qfile_out">
164 <assert_contents>
165 <expand macro="test-qfile-format"/>
166 <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>
167 </assert_contents>
168 </output>
169 <output name="fastq_scrap_out">
170 <assert_contents>
171 <expand macro="test-fastq-format"/>
172 <has_text text="@M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
173 </assert_contents>
174 </output>
175 <output name="fasta_scrap_out">
176 <assert_contents>
177 <expand macro="test-fasta-format"/>
178 </assert_contents>
179 </output>
180 <output name="qfile_scrap_out">
181 <assert_contents>
182 <expand macro="test-qfile-format"/>
183 <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>
184 </assert_contents>
185 </output>
186 <param name="savelog" value="true"/>
123 <expand macro="logfile-test"/> 187 <expand macro="logfile-test"/>
124 </test> 188 </test>
125 </tests> 189 </tests>
126 <help> 190 <help><![CDATA[
127 <![CDATA[
128 191
129 @MOTHUR_OVERVIEW@ 192 @MOTHUR_OVERVIEW@
130 193
131 **Command Documentation** 194 **Command Documentation**
132 195
133 The fastq.info_ command reads a fastq file and creates a fasta and quality file. 196 The fastq.info_ command reads a fastq file and creates a fasta and quality file.
134 197
135 198
136 .. _fastq.info: https://www.mothur.org/wiki/Fastq.info 199 .. _fastq.info: https://www.mothur.org/wiki/Fastq.info
137 ]]> 200
138 </help> 201 ]]></help>
139 <expand macro="citations"/> 202 <expand macro="citations"/>
140 </tool> 203 </tool>