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comparison macros.xml @ 0:099a35a39c29 draft default tip

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"planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
author jjohnson
date Thu, 19 Aug 2021 15:13:55 +0000
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-1:000000000000 0:099a35a39c29
1 <macros>
2 <token name="@TOOL_VERSION@">1.3.0</token>
3 <token name="@VERSION_SUFFIX@">1</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement>
7 <yield/>
8 </requirements>
9 </xml>
10 <xml name="citations">
11 <citations>
12 <citation type="bibtex">@online{fgbio,
13 author = {Tim Fennell, Nils Homer},
14 title = {fgbio},
15 year = 2015,
16 url = {https://github.com/fulcrumgenomics/fgbio},
17 urldate = {2021-03-01}
18 }</citation>
19 </citations>
20 </xml>
21 <token name="@READ_STRUCTURE_PATTERN@">(([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS])</token>
22 <token name="@READ_STRUCTURES_PATTERN@">@READ_STRUCTURE_PATTERN@(\s@READ_STRUCTURE_PATTERN@)*</token>
23 <xml name="read_structures_validator" token_pattern="@READ_STRUCTURES_PATTERN@">
24 <validator type="regex" message="">^@READ_STRUCTURES_PATTERN@$</validator>
25 </xml>
26 <xml name="read_structures" token_pattern="@READ_STRUCTURES_PATTERN@">
27 <param argument="--read-structures" type="text" value="" optional="true" label="Read structures, one for each of the FASTQ">
28 <expand macro="read_structures_validator" pattern="@READ_STRUCTURE_PATTERN@" />
29 </param>
30 </xml>
31
32 <xml name="fastq_input" token_fastqtype="reads" token_defaultpaired="True" token_defaultnone="False">
33 <conditional name="@FASTQTYPE@">
34 <param name="type" type="select" label="Library type of FASTQ @FASTQTYPE@">
35 <option value="none" selected="@DEFAULTNONE@">NO fastq @FASTQTYPE@</option>
36 <option value="single">Single-end</option>
37 <option value="paired" selected="@DEFAULTPAIRED@">Paired-end</option>
38 <option value="paired_collection">Paired-end Dataset Collection</option>
39 </param>
40 <when value="none"/>
41 <when value="single">
42 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
43 <expand macro="read_structures" pattern="@READ_STRUCTURE_PATTERN@" />
44 </when>
45 <when value="paired">
46 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads #1 in FASTQ format" />
47 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads #2 in FASTQ format" />
48 <expand macro="read_structures" pattern="@READ_STRUCTURES_PATTERN@" />
49 </when>
50 <when value="paired_collection">
51 <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired Reads in FASTQ format" />
52 <expand macro="read_structures" pattern="@READ_STRUCTURES_PATTERN@" />
53 </when>
54 </conditional>
55 </xml>
56 <xml name="fastq_reads">
57 <expand macro="fastq_input" fastqtype="reads" defaultpaired="True" defaultnone="False"/>
58 </xml>
59 <xml name="fastq_inputs">
60 <expand macro="fastq_input" fastqtype="reads" defaultpaired="True" defaultnone="False"/>
61 <expand macro="fastq_input" fastqtype="indices" defaultpaired="False" defaultnone="True"/>
62 </xml>
63 <token name="@FASTQ_READS@"><![CDATA[
64 #set $fastqs = []
65 #set $read_structs = []
66 #if $reads.type == 'single':
67 $fastqs.append($reads.input_single)
68 #elif $reads.type == 'paired':
69 $fastqs.append($reads.input_read1)
70 $fastqs.append($reads.input_read2)
71 #elif $reads.type == 'paired_collection':
72 $fastqs.append($reads.input_readpair.forward)
73 $fastqs.append($reads.input_readpair.reverse)
74 #end if
75 #if $reads.type !='none' and $reads.read_structures:
76 $read_structs.append(str($reads.read_structures))
77 #end if
78 #set $read_structures = "%s" % (' '.join($read_structs))
79 #if $read_structs:
80 --read-structures $read_structures
81 #end if
82 ]]></token>
83 <token name="@LINK_FASTQ_INPUTS@"><![CDATA[
84 #import re
85 #def identifier_or_name($input1)
86 #if hasattr($input1, 'element_identifier')
87 #return $input1.element_identifier
88 #else
89 #return $input1.name
90 #end if
91 #end def
92 #def clean($name1)
93 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fq|fastq)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
94 #return $name_clean
95 #end def
96 #def ln_name($ds)
97 #set $ext = ''
98 #if $ds.is_of_type('mzml') or $ds.is_of_type('fastq.gz')
99 #set $ext = ".fastq.gz"
100 #else if $ds.is_of_type('fastq')
101 #set $ext = ".fastq"
102 #end if
103 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
104 #return $name
105 #end def
106 #set $fastqs = []
107 #set $read_structs = []
108 #if $reads.type == 'single':
109 #set $i_name = $ln_name($reads.input_single)
110 #silent $fastqs.append($i_name)
111 ln -s '$reads.input_single' '$i_name' &&
112 #elif $reads.type == 'paired':
113 #set $f_name = $ln_name($reads.input_read1)
114 #silent $fastqs.append($f_name)
115 ln -s '$reads.input_read1' '$f_name' &&
116 #set $r_name = $ln_name($reads.input_read2)
117 #silent $fastqs.append($r_name)
118 ln -s '$reads.input_read2' '$r_name' &&
119 #elif $reads.type == 'paired_collection':
120 #set $f_name = $ln_name($reads.input_readpair.forward)
121 #silent $fastqs.append($f_name)
122 ln -s '$reads.input_readpair.forward' '$f_name' &&
123 #set $r_name = $ln_name($reads.input_readpair.reverse)
124 #silent $fastqs.append($r_name)
125 ln -s '$reads.input_readpair.reverse' '$r_name' &&
126 #end if
127 #if $reads.type !='none' and $reads.read_structures:
128 $read_structs.append(str($reads.read_structures))
129 #end if
130 #if $indices.type == 'single':
131 #set $i_name = $ln_name($indices.input_single)
132 #silent $fastqs.append($i_name)
133 ln -s '$indices.input_single' '$i_name' &&
134 #elif $indices.type == 'paired':
135 #set $f_name = $ln_name($indices.input_read1)
136 #silent $fastqs.append($f_name)
137 ln -s '$indices.input_read1' '$f_name' &&
138 #set $r_name = $ln_name($indices.input_read2)
139 #silent $fastqs.append($r_name)
140 ln -s '$indices.input_read2' '$r_name' &&
141 #elif $indices.type == 'paired_collection':
142 #set $f_name = $ln_name($indices.input_readpair.forward)
143 #silent $fastqs.append($f_name)
144 ln -s '$indices.input_readpair.forward' '$f_name' &&
145 #set $r_name = $ln_name($indices.input_readpair.reverse)
146 #silent $fastqs.append($r_name)
147 ln -s '$indices.input_readpair.reverse' '$r_name' &&
148 #end if
149 #if $indices.type != 'none' and $indices.read_structures:
150 $read_structs.append(str($indices.read_structures))
151 #end if
152 ]]></token>
153 <token name="@FASTQ_INPUTS@"><![CDATA[
154 --input
155 #for $input in $fastqs
156 '$input'
157 #end for
158 #set $read_structures = "%s" % (' '.join($read_structs))
159 #if $read_structs:
160 --read-structures $read_structures
161 #end if
162 ]]></token>
163 <xml name="inherit_format_1">
164 <actions>
165 <conditional name="library.type">
166 <when value="single">
167 <action type="format">
168 <option type="from_param" name="library.input_1" param_attribute="ext" />
169 </action>
170 </when>
171 <when value="paired">
172 <action type="format">
173 <option type="from_param" name="library.input_1" param_attribute="ext" />
174 </action>
175 </when>
176 <when value="paired_collection">
177 <action type="format">
178 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
179 </action>
180 </when>
181 </conditional>
182 </actions>
183 </xml>
184
185 <xml name="inherit_format_2">
186 <actions>
187 <conditional name="library.type">
188 <when value="paired">
189 <action type="format">
190 <option type="from_param" name="library.input_2" param_attribute="ext" />
191 </action>
192 </when>
193 <when value="paired_collection">
194 <action type="format">
195 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
196 </action>
197 </when>
198 </conditional>
199 </actions>
200 </xml>
201 <xml name="sam_tag_validator">
202
203 <validator type="regex" message="">^[A-Za-z][A-Za-z]$</validator>
204 </xml>
205 <xml name="sam_sort_order">
206 <param argument="--sort-order" type="select" optional="true" label="Sort BAM by">
207 <option value="TemplateCoordinate">TemplateCoordinate</option>
208 <option value="Coordinate">Coordinate</option>
209 <option value="Queryname">Queryname</option>
210 <option value="Random">Random</option>
211 <option value="RandomQuery">RandomQuery</option>
212 </param>
213 </xml>
214
215 <xml name="sort_order_change_format">
216 <change_format>
217 <when input="sort_order" value="Coordinate" format="bam" />
218 <when input="sort_order" value="TemplateCoordinate" format="bam" />
219 <when input="sort_order" value="QueryName" format="unsorted.bam" />
220 <when input="sort_order" value="Random" format="unsorted.bam" />
221 <when input="sort_order" value="RandomQuery" format="unsorted.bam" />
222 </change_format>
223 </xml>
224
225 <token name="@READ_STRUCTURES_HELP@"><![CDATA[
226 **Read Structures**
227
228 Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:
229
230 - T identifies a template read
231 - B identifies a sample barcode read
232 - M identifies a unique molecular index read
233 - S identifies a set of bases that should be skipped or ignored
234
235 The last <number><operator> pair may be specified using a + sign instead of number to denote “all remaining bases”. This is useful if, e.g., fastqs have been trimmed and contain reads of varying length. For example to convert a paired-end run with an index read and where the first 5 bases of R1 are a UMI and the second five bases are monotemplate you might specify:
236
237 ::
238
239 --input r1.fq r2.fq i1.fq --read-structures 5M5S+T +T +B
240
241 Alternative if you know your reads are of fixed length you could specify:
242
243 ::
244
245 --input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B
246
247
248 ]]></token>
249 <xml name="citations">
250 <citations>
251 <yield />
252 </citations>
253 </xml>
254 </macros>