Mercurial > repos > matthias > stacks2_refmap

comparison macros.xml @ 3:93fb82c0fc94 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/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
author matthias
date Tue, 18 Dec 2018 12:48:09 -0500
parents 39ebc7633942
children e1dbdd7175c8
comparison
equal deleted inserted replaced
2:39ebc7633942 3:93fb82c0fc94
6 <yield/> 6 <yield/>
7 </requirements> 7 </requirements>
8 </xml> 8 </xml>
9 9
10 <token name="@STACKS_VERSION@">2.2</token> 10 <token name="@STACKS_VERSION@">2.2</token>
11 <token name="@WRAPPER_VERSION@">1</token> 11 <token name="@WRAPPER_VERSION@">2</token>
12 12
13 <xml name="stdio"> 13 <xml name="stdio">
14 <stdio> 14 <stdio>
15 <exit_code range="1:" level="fatal" description="Error in Stacks execution" /> 15 <exit_code range="1:" level="fatal" description="Error in Stacks execution" />
16 </stdio> 16 </stdio>
126 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file"> 126 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file">
127 <filter>add_log</filter> 127 <filter>add_log</filter>
128 </data> 128 </data>
129 </xml> 129 </xml>
130 130
131
131 <!-- fastq input --> 132 <!-- fastq input -->
132 <xml name="fastq_input_macro" token_fastq_optional="false"> 133 <xml name="fastq_input_macro" token_fastq_optional="false">
133 <conditional name="input_type"> 134 <conditional name="input_type">
134 <param name="input_type_selector" type="select" label="Short read data from individuals" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks"> 135 <param name="input_type_selector" type="select" label="Short read data from individuals" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks">
135 <option value="manual" selected="true">single end or forward reads</option> 136 <option value="manual" selected="true">single end or forward reads</option>
137 </param> 138 </param>
138 <when value="manual"> 139 <when value="manual">
139 <param name="samples" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/> 140 <param name="samples" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/>
140 </when> 141 </when>
141 <when value="list"> 142 <when value="list">
142 <param name="samples" argument="-f" type="data_collection" collection_type="list,list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/> 143 <param name="samples" argument="-f" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/>
143 </when> 144 </when>
144 </conditional> 145 </conditional>
145 </xml> 146 </xml>
146 <!-- requires a variable $read_direction=None|"forward"|"reverse" to be set 147 <!-- requires a variable $read_direction=None|"forward"|"reverse" to be set
147 appends noting/.1/.2 to the link name for accessing the fastq data 148 appends noting/.1/.2 to the link name for accessing the fastq data
148 sets variables $name and $data_path--> 149 sets variables $name and $data_path-->
149 <token name="@FASTQ_INPUT@"><![CDATA[ 150 <token name="@FASTQ_INPUT@"><![CDATA[
151 ## TODO should use sample.identidfier if possible (see corresp. preproc macro)
150 #set $name = $clean_ext($sample.name) 152 #set $name = $clean_ext($sample.name)
151 #set $data_path = "stacks_inputs/" + $name 153 #set $data_path = "stacks_inputs/" + $name
152 #if $sample.is_collection: 154 #if $sample.is_collection:
153 #set $sample=$sample[$read_direction] 155 #set $cur_sample=$sample[$read_direction]
156 #else:
157 #set $cur_sample=$sample
154 #end if 158 #end if
155 #if $read_direction == "forward": 159 #if $read_direction == "forward":
156 #set $data_path = $data_path + ".1" 160 #set $data_path = $data_path + ".1"
157 #elif $read_direction == "reverse": 161 #elif $read_direction == "reverse":
158 #set $data_path = $data_path + ".2" 162 #set $data_path = $data_path + ".2"
159 #end if 163 #end if
160 #if $sample.is_of_type('fastqsanger') 164 #if $cur_sample.is_of_type('fastqsanger')
161 #set $data_path = $data_path + ".fq" 165 #set $data_path = $data_path + ".fq"
162 #set inputype = "fastq" 166 #set inputype = "fastq"
163 #else if $sample.is_of_type('fastqsanger.gz') 167 #else if $cur_sample.is_of_type('fastqsanger.gz')
164 #set $data_path = $data_path + ".fq.gz" 168 #set $data_path = $data_path + ".fq.gz"
165 #set inputype = "gzfastq" 169 #set inputype = "gzfastq"
166 #else if $sample.is_of_type('fasta') 170 #else if $cur_sample.is_of_type('fasta')
167 #set $data_path = $data_path + ".fa" 171 #set $data_path = $data_path + ".fa"
168 #set inputype = "fasta" 172 #set inputype = "fasta"
169 #else 173 #else
170 #set $data_path = $data_path + ".fa.gz" 174 #set $data_path = $data_path + ".fa.gz"
171 #set inputype = "gzfasta" 175 #set inputype = "gzfasta"
172 #end if 176 #end if
173 ln -s '$sample' '${data_path}' && 177 ln -s '$cur_sample' '${data_path}' &&
174 ]]></token> 178 ]]></token>
175 179
176 <!-- macro and token for BAM input--> 180 <!-- macro and token for BAM input-->
177 <xml name="bam_input_macro"> 181 <xml name="bam_input_macro">
178 <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" /> 182 <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" />
186 #set bamlist += " -B 'bam_inputs/"+$filename+"'" 190 #set bamlist += " -B 'bam_inputs/"+$filename+"'"
187 #end if 191 #end if
188 #end for 192 #end for
189 ]]></token> 193 ]]></token>
190 194
191 <xml name="discover_faqgz_output_macro" token_pattern="" token_dir="">
192 <expand macro="discover_faq_output_macro" pattern="@PATTERN@" dir="@DIR@"/>
193 <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/" />
194 <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/" />
195 </xml>
196 <xml name="discover_faq_output_macro" token_pattern="" token_dir="">
197 <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/" />
198 <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/" />
199 </xml>
200 <token name="@CLEAN_EXT@"> 195 <token name="@CLEAN_EXT@">
201 <![CDATA[ 196 <![CDATA[
202 #from os.path import splitext 197 #from os.path import splitext
203 #import re 198 #import re
204 #def clean_ext($identifier) 199 #def clean_ext($identifier)
410 </xml> 405 </xml>
411 <xml name="variant_calling_options_g"> 406 <xml name="variant_calling_options_g">
412 <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="alpha threshold for calling genotypes" /> 407 <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="alpha threshold for calling genotypes" />
413 </xml> 408 </xml>
414 409
415 <xml name="barcode_encoding_single"> 410 <xml name="barcode_encoding_single" token_type="">
416 <option value="--inline_null" selected="True">Barcode is inline with sequence, occurs only on single-end read</option> 411 <option value="--inline_null" selected="True">@TYPE@ is inline with sequence, occurs only on single-end read (--inline_null)</option>
417 <option value="--index_null">Barcode is provded in FASTQ header (Illumina i5 or i7 read)</option> 412 <option value="--index_null">@TYPE@ is provded in FASTQ header (Illumina i5 or i7 read) (--index_null)</option>
418 <yield/> 413 <yield/>
419 </xml> 414 </xml>
420 415
421 <xml name="barcode_encoding_pair"> 416 <xml name="barcode_encoding_pair" token_type="">
422 <expand macro="barcode_encoding_single"> 417 <expand macro="barcode_encoding_single" type="@TYPE@">
423 <option value="--null_index">barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided)</option> 418 <option value="--null_index">@TYPE@ is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided) (--null_index)</option>
424 <option value="--inline_inline">barcode is inline with sequence, occurs on single and paired-end read</option> 419 <option value="--inline_inline">@TYPE@ is inline with sequence, occurs on single and paired-end read (--inline_inline)</option>
425 <option value="--index_index">barcode is provded in FASTQ header (Illumina i5 and i7 reads).</option> 420 <option value="--index_index">@TYPE@ is provded in FASTQ header (Illumina i5 and i7 reads) (--index_index)</option>
426 <option value="--inline_index">barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read)</option> 421 <option value="--inline_index">@TYPE@ is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read) (--inline_index)</option>
427 <option value="--index_inline"></option> 422 <option value="--index_inline">@TYPE@ occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data) (--index_inline)</option>
428 </expand> 423 </expand>
429 </xml> 424 </xml>
430 </macros> 425 </macros>