Mercurial > repos > iuc > stacks_procrad

comparison stacks_procrad.xml @ 8:bec1f08cdfcc 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/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
author iuc
date Thu, 27 Apr 2017 04:19:34 -0400
parents 2837e6ae4e18
children 57910d476be9
comparison
equal deleted inserted replaced
7:f1f715f5d2f3 8:bec1f08cdfcc
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <command><![CDATA[ 8 <command><![CDATA[
9 9
10 #if $input_type.options_type_selector == "single": 10 #if $input_type.options_type_selector == "single"
11 11
12 #if $input_type.input_single.is_of_type('fastqsanger'): 12 #if $input_type.input_single.is_of_type('fastqsanger')
13 #set $ext = ".fq" 13 #set $ext = ".fq"
14 #set inputype = "fastq" 14 #set inputype = "fastq"
15 #else: 15 #else
16 #set $ext = ".fq.gz" 16 #set $ext = ".fq.gz"
17 #set inputype = "gzfastq" 17 #set inputype = "gzfastq"
18 #end if 18 #end if
19 19
20 ln -s "$input_type.input_single" R1$ext && 20 ln -s '$input_type.input_single' R1$ext &&
21 #else 21 #else
22 22
23 #if $input_type.inputs_paired1.is_of_type('fastqsanger'): 23 #if $input_type.inputs_paired1.is_of_type('fastqsanger')
24 #set $ext = ".fq" 24 #set $ext = ".fq"
25 #set inputype = "fastq" 25 #set inputype = "fastq"
26 #else: 26 #else
27 #set $ext = ".fq.gz" 27 #set $ext = ".fq.gz"
28 #set inputype = "gzfastq" 28 #set inputype = "gzfastq"
29 #end if 29 #end if
30 30
31 ln -s "$input_type.inputs_paired1" R1$ext && 31 ln -s '$input_type.inputs_paired1' R1$ext &&
32 ln -s "$input_type.inputs_paired2" R2$ext && 32 ln -s '$input_type.inputs_paired2' R2$ext &&
33 #end if 33 #end if
34 34
35 mkdir stacks_outputs 35 mkdir stacks_outputs
36 36
37 && 37 &&
38 38
39 process_radtags 39 process_radtags
40 40
41 #if $input_type.options_type_selector == "single": 41 #if $input_type.options_type_selector == "single"
42 -f R1$ext 42 -f R1$ext
43 #else: 43 #else
44 -1 R1$ext 44 -1 R1$ext
45 -2 R2$ext 45 -2 R2$ext
46 #end if 46 #end if
47 47
48 -i $inputype 48 -i $inputype
49 -b "$barcode" 49 -b '$barcode'
50 50
51 $input_type.barcode_encoding 51 $input_type.barcode_encoding
52 52
53 #if str( $options_enzyme.options_enzyme_selector ) == "1": 53 #if str( $options_enzyme.options_enzyme_selector ) == "1"
54 -e $options_enzyme.enzyme 54 -e $options_enzyme.enzyme
55 #else: 55 #else
56 --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2 56 --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2
57 #end if 57 #end if
58 58
59 -y $outype 59 #if str( $outype ) != "auto"
60 -y $outype
61 #end if
60 62
61 $capture 63 $capture
62 64
63 $options_advanced.retain_header 65 $options_advanced.retain_header
64 66
65 #if str($options_advanced.truncate): 67 #if str($options_advanced.truncate)
66 -t $options_advanced.truncate 68 -t $options_advanced.truncate
67 #end if 69 #end if
68 70
69 -w $options_advanced.sliding 71 -w $options_advanced.sliding
70 72
83 <param name="options_type_selector" type="select" label="Single-end or paired-end reads files"> 85 <param name="options_type_selector" type="select" label="Single-end or paired-end reads files">
84 <option value="single" selected="True">Single-end files</option> 86 <option value="single" selected="True">Single-end files</option>
85 <option value="paired">Paired-end files</option> 87 <option value="paired">Paired-end files</option>
86 </param> 88 </param>
87 <when value="single"> 89 <when value="single">
88 <param name="input_single" argument="-f" format="fastqsanger,fastq.gz" type="data" label="singles-end reads infile(s)" help="input files" /> 90 <param name="input_single" argument="-f" format="fastqsanger,fastqsanger.gz" type="data" label="singles-end reads infile(s)" help="input files" />
89 91
90 <param name="barcode_encoding" type="select" label="Barcode location"> 92 <param name="barcode_encoding" type="select" label="Barcode location">
91 <option value="--inline_null" selected="True">Barcode is inline with sequence</option> 93 <option value="--inline_null" selected="True">Barcode is inline with sequence</option>
92 <option value="--index_null">Barcode is provided in FASTQ header</option> 94 <option value="--index_null">Barcode is provided in FASTQ header</option>
93 </param> 95 </param>
94 </when> 96 </when>
95 <when value="paired"> 97 <when value="paired">
96 <param name="inputs_paired1" argument="-1" format="fastqsanger,fastq.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" /> 98 <param name="inputs_paired1" argument="-1" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" />
97 <param name="inputs_paired2" argument="-2" format="fastqsanger,fastq.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" /> 99 <param name="inputs_paired2" argument="-2" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" />
98 100
99 <param name="barcode_encoding" type="select" label="Barcode location"> 101 <param name="barcode_encoding" type="select" label="Barcode location">
100 <option value="--inline_null" selected="True">Barcode is inline with sequence, only on the single-end read (read 1)</option> 102 <option value="--inline_null" selected="True">Barcode is inline with sequence, only on the single-end read (read 1)</option>
101 <option value="--index_null">Barcode is provided in FASTQ header, only on the single-end read (read 1)</option> 103 <option value="--index_null">Barcode is provided in FASTQ header, only on the single-end read (read 1)</option>
102 <option value="--inline_inline">Barcode is inline with sequence, on both single and paired-end read (read 1 and 2)</option> 104 <option value="--inline_inline">Barcode is inline with sequence, on both single and paired-end read (read 1 and 2)</option>
139 <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/> 141 <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/>
140 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" /> 142 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />
141 <param name="retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" /> 143 <param name="retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" />
142 </section> 144 </section>
143 145
144 <!-- Stacks can produce fastq.gz and fasta.gz output but we don't propose it as they are not very common datatypes in galaxy --> 146 <param name="outype" argument="-y" type="select" label="Output format" >
145 <param name="outype" argument="-y" type="select" label="Output format" help="output type, either 'fastq' or 'fasta'" > 147 <option value="auto" selected="True">Same as input</option>
146 <option value="fastq" selected="True">fastq</option> 148 <option value="fastq">fastq</option>
147 <option value="fasta">fasta</option> 149 <option value="fasta">fasta</option>
150 <option value="gzfastq">gzipped fastq</option>
148 </param> 151 </param>
149 </inputs> 152 </inputs>
150 153
151 <outputs> 154 <outputs>
152 <data format="txt" name="output_log" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" from_work_dir="stacks_outputs/process_radtags.log" /> 155 <data format="txt" name="output_log" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" from_work_dir="stacks_outputs/process_radtags.log" />
153 156
154 <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}"> 157 <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}">
155 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" /> 158 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
159 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" />
156 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" /> 160 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
157 </collection> 161 </collection>
158 <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}"> 162 <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}">
159 <filter>input_type['options_type_selector'] == "paired"</filter> 163 <filter>input_type['options_type_selector'] == "paired"</filter>
160 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" /> 164 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
165 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" />
161 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" /> 166 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
162 </collection> 167 </collection>
163 <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}"> 168 <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}">
164 <filter>capture is True</filter> 169 <filter>capture is True</filter>
165 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" /> 170 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" />
171 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fq\.gz.discards$" ext="fastqsanger" directory="stacks_outputs" /> <!-- discards are never gzipped -->
166 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" /> 172 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" />
167 </collection> 173 </collection>
168 </outputs> 174 </outputs>
169 175
170 <tests> 176 <tests>
187 </assert_contents> 193 </assert_contents>
188 </element> 194 </element>
189 </output_collection> 195 </output_collection>
190 </test> 196 </test>
191 <test> 197 <test>
198 <param name="options_type_selector" value="single"/>
199 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/>
200 <param name="barcode" value="procrad/barcodes"/>
201 <param name="options_enzyme_selector" value="1"/>
202 <param name="enzyme" value="ecoRI"/>
203 <param name="discard" value="true"/>
204 <param name="capture" value="true"/>
205 <param name="outype" value="gzfastq"/>
206 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
207 <output_collection name="demultiplexed">
208 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/>
209 </output_collection>
210 <output_collection name="discarded">
211 <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/>
212 </output_collection>
213 </test>
214 <test>
192 <param name="options_type_selector" value="paired"/> 215 <param name="options_type_selector" value="paired"/>
193 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/> 216 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
194 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/> 217 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
195 <param name="barcode" value="procrad/barcodes"/> 218 <param name="barcode" value="procrad/barcodes"/>
196 <param name="options_enzyme_selector" value="1"/> 219 <param name="options_enzyme_selector" value="1"/>
258 <element name="R1"> 281 <element name="R1">
259 <assert_contents> 282 <assert_contents>
260 <has_text text="lane1_fakedata0_11" /> 283 <has_text text="lane1_fakedata0_11" />
261 </assert_contents> 284 </assert_contents>
262 </element> 285 </element>
286 </output_collection>
287 </test>
288 <test>
289 <param name="options_type_selector" value="single"/>
290 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq.gzip"/>
291 <param name="barcode" value="procrad/barcodes"/>
292 <param name="options_enzyme_selector" value="1"/>
293 <param name="enzyme" value="ecoRI"/>
294 <param name="discard" value="true"/>
295 <param name="capture" value="true"/>
296 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
297 <output_collection name="demultiplexed">
298 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>
299 </output_collection>
300 <output_collection name="discarded">
301 <element name="R1">
302 <assert_contents>
303 <has_text text="lane1_fakedata0_11" />
304 </assert_contents>
305 </element>
306 </output_collection>
307 </test>
308 <test>
309 <param name="options_type_selector" value="single"/>
310 <param name="input_single" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip"/>
311 <param name="barcode" value="procrad/barcodes"/>
312 <param name="options_enzyme_selector" value="1"/>
313 <param name="enzyme" value="ecoRI"/>
314 <param name="discard" value="true"/>
315 <param name="capture" value="true"/>
316 <param name="outype" value="gzfastq"/>
317 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
318 <output_collection name="demultiplexed">
319 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq.gzip"/>
320 </output_collection>
321 <output_collection name="discarded">
322 <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/>
263 </output_collection> 323 </output_collection>
264 </test> 324 </test>
265 </tests> 325 </tests>
266 326
267 327