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comparison bwa.xml @ 2:b4dfb5470bf3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
author devteam
date Fri, 30 Dec 2016 08:10:56 -0500
parents 8955a9521def
children 0bde88ff668c
comparison
equal deleted inserted replaced
1:8955a9521def 2:b4dfb5470bf3
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bwa" name="Map with BWA" version="0.4.2"> 2 <tool id="bwa" name="Map with BWA" version="@VERSION@.1">
3 <description>- map short reads (&lt; 100 bp) against reference genome</description> 3 <description>- map short reads (&lt; 100 bp) against reference genome</description>
4 <macros> 4 <macros>
5 <import>read_group_macros.xml</import> 5 <import>read_group_macros.xml</import>
6 <import>bwa_macros.xml</import> 6 <import>bwa_macros.xml</import>
7 <token name="@command_options@"> 7 <token name="@command_options@">
66 </xml> 66 </xml>
67 </macros> 67 </macros>
68 <expand macro="requirements" /> 68 <expand macro="requirements" />
69 <expand macro="stdio" /> 69 <expand macro="stdio" />
70 <command> 70 <command>
71 #set $reference_fasta_filename = "localref.fa" 71 <![CDATA[
72 72 @set_reference_fasta_filename@
73 #if str( $reference_source.reference_source_selector ) == "history":
74 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
75
76 ## The following shell commands decide with of the BWA indexing algorithms (IS or BWTSW) will be run
77 ## depending ob the size of the input FASTA dataset
78 (
79 size=`stat -c %s "${reference_fasta_filename}" 2&gt;/dev/null`; ## Linux
80 if [ $? -eq 0 ];
81 then
82 if [ "\$size" -lt 2000000000 ];
83 then
84 bwa index -a is "${reference_fasta_filename}";
85 else
86 bwa index -a bwtsw "${reference_fasta_filename}";
87 fi;
88 fi;
89
90 eval \$(stat -s "${reference_fasta_filename}" 2&gt;/dev/null); ## OSX
91 if [ -n "\$st_size" ];
92 then
93 if [ "\$st_size" -lt 2000000000 ];
94 then
95 bwa index -a is "${reference_fasta_filename}";
96 echo "Generating BWA index with is algorithm";
97 else
98 bwa index -a bwtsw "${reference_fasta_filename}";
99 echo "Generating BWA index with bwtsw algorithm";
100 fi;
101 fi;
102 ) &amp;&amp;
103 #else:
104 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
105 #end if
106 73
107 ## setup vars for rg handling... 74 ## setup vars for rg handling...
108 @define_read_group_helpers@ 75 @define_read_group_helpers@
109 #if str( $input_type.input_type_selector ) == "paired": 76 #if str( $input_type.input_type_selector ) == "paired":
110 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1, $input_type.fastq_input2) 77 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1, $input_type.fastq_input2)
132 "${input_type.fastq_input1.forward}" 99 "${input_type.fastq_input1.forward}"
133 #else 100 #else
134 "${input_type.fastq_input1}" 101 "${input_type.fastq_input1}"
135 #end if 102 #end if
136 103
137 > first.sai &amp;&amp; 104 > first.sai &&
138 105
139 bwa aln 106 bwa aln
140 -t "\${GALAXY_SLOTS:-1}" 107 -t "\${GALAXY_SLOTS:-1}"
141 108
142 @command_options@ 109 @command_options@
147 "${input_type.fastq_input1.reverse}" 114 "${input_type.fastq_input1.reverse}"
148 #else 115 #else
149 "${input_type.fastq_input2}" 116 "${input_type.fastq_input2}"
150 #end if 117 #end if
151 118
152 > second.sai &amp;&amp; 119 > second.sai &&
153 120
154 bwa sampe 121 bwa sampe
155 122
156 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True": 123 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True":
157 -a ${$input_type.adv_pe_options.a} 124 -a ${$input_type.adv_pe_options.a}
176 143
177 @command_options@ 144 @command_options@
178 145
179 "${reference_fasta_filename}" 146 "${reference_fasta_filename}"
180 "${input_type.fastq_input1}" 147 "${input_type.fastq_input1}"
181 > first.sai &amp;&amp; 148 > first.sai &&
182 149
183 bwa samse 150 bwa samse
184 151
185 #if str( $input_type.adv_se_options.adv_se_options_selector) == "True": 152 #if str( $input_type.adv_se_options.adv_se_options_selector) == "True":
186 -n ${$input_type.adv_se_options.n} 153 -n ${$input_type.adv_se_options.n}
200 167
201 @command_options@ 168 @command_options@
202 169
203 "${reference_fasta_filename}" 170 "${reference_fasta_filename}"
204 "${input_type.bam_input}" 171 "${input_type.bam_input}"
205 > first.sai &amp;&amp; 172 > first.sai &&
206 173
207 bwa aln 174 bwa aln
208 -t "\${GALAXY_SLOTS:-1}" 175 -t "\${GALAXY_SLOTS:-1}"
209 -b 176 -b
210 -2 177 -2
211 @command_options@ 178 @command_options@
212 "${reference_fasta_filename}" 179 "${reference_fasta_filename}"
213 "${input_type.bam_input}" 180 "${input_type.bam_input}"
214 > second.sai &amp;&amp; 181 > second.sai &&
215 182
216 bwa sampe 183 bwa sampe
217 184
218 #if str( $input_type.adv_bam_pe_options.adv_pe_options_selector) == "True": 185 #if str( $input_type.adv_bam_pe_options.adv_pe_options_selector) == "True":
219 -a ${$input_type.adv_bam_pe_options.a} 186 -a ${$input_type.adv_bam_pe_options.a}
236 203
237 @command_options@ 204 @command_options@
238 205
239 "${reference_fasta_filename}" 206 "${reference_fasta_filename}"
240 "${input_type.bam_input}" 207 "${input_type.bam_input}"
241 > first.sai &amp;&amp; 208 > first.sai &&
242 209
243 bwa samse 210 bwa samse
244 211
245 #if str( $input_type.adv_bam_se_options.adv_se_options_selector) == "True": 212 #if str( $input_type.adv_bam_se_options.adv_se_options_selector) == "True":
246 -n ${$input_type.adv_bam_se_options.n} 213 -n ${$input_type.adv_bam_se_options.n}
249 @read_group_options@ 216 @read_group_options@
250 217
251 "${reference_fasta_filename}" first.sai "${input_type.bam_input}" 218 "${reference_fasta_filename}" first.sai "${input_type.bam_input}"
252 #end if 219 #end if
253 220
254 | samtools view -Sb - > temporary_bam_file.bam &amp;&amp; 221 | samtools sort -O bam -o '$bam_output'
255 222 ]]>
256 samtools sort -f temporary_bam_file.bam ${bam_output}
257 </command> 223 </command>
258 224
259 <inputs> 225 <inputs>
260 226 <expand macro="reference_source_conditional" />
261 <conditional name="reference_source">
262 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
263 <option value="cached">Use a built-in genome index</option>
264 <option value="history">Use a genome from history and build index</option>
265 </param>
266 <when value="cached">
267 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
268 <options from_data_table="bwa_mem_indexes">
269 <filter type="sort_by" column="2" />
270 <validator type="no_options" message="No indexes are available" />
271 </options>
272 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
273 </param>
274 </when>
275 <when value="history">
276 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
277 </when>
278 </conditional>
279 <conditional name="input_type"> 227 <conditional name="input_type">
280 <param name="input_type_selector" type="select" label="Select input type" help="Select between fastq and bam datasets and between paired and single end data"> 228 <param name="input_type_selector" type="select" label="Select input type" help="Select between fastq and bam datasets and between paired and single end data">
281 <option value="paired">Paired fastq</option> 229 <option value="paired">Paired fastq</option>
282 <option value="paired_collection">Paired fastq collection</option> 230 <option value="paired_collection">Paired fastq collection</option>
283 <option value="single">Single fastq</option> 231 <option value="single">Single fastq</option>