Mercurial > repos > devteam > bwa

comparison bwa.xml @ 10:6069ffa8b240 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-devteam/tree/master/tools/bwa commit 653588a3c59eb9965097f87c99e6fca1806365cd
author devteam
date Fri, 08 Jan 2016 17:02:09 -0500
parents 7bee165c3a44
children 546ada4a9f43
comparison
equal deleted inserted replaced
9:7bee165c3a44 10:6069ffa8b240
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="0.7.12">
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 <![CDATA[
71 #set $reference_fasta_filename = "localref.fa" 72 #set $reference_fasta_filename = "localref.fa"
72 73
73 #if str( $reference_source.reference_source_selector ) == "history": 74 #if str( $reference_source.reference_source_selector ) == "history":
74 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp; 75 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
75 76
76 ## The following shell commands decide with of the BWA indexing algorithms (IS or BWTSW) will be run 77 ## The following shell commands decide which of the BWA indexing algorithms (IS or BWTSW) will be run
77 ## depending ob the size of the input FASTA dataset 78 ## depending on the size of the input FASTA dataset
78 ( 79 ( size=`stat -c %s "${reference_source.ref_file}" 2>/dev/null`; ## Linux
79 size=`stat -c %s "${reference_fasta_filename}" 2&gt;/dev/null`; ## Linux 80 if [ $? -ne 0 ]; then
80 if [ $? -eq 0 ]; 81 size=\$(stat -f %z "${reference_source.ref_file}"); ## OSX
81 then 82 fi &&
82 if [ "\$size" -lt 2000000000 ]; 83 if [ "\$size" -lt 2000000000 ]; then
83 then 84 echo "Reference genome size is \$size bytes, generating BWA index with is algorithm";
84 bwa index -a is "${reference_fasta_filename}"; 85 bwa index -a is "${reference_fasta_filename}";
85 else 86 else
86 bwa index -a bwtsw "${reference_fasta_filename}"; 87 echo "Reference genome size is \$size bytes, generating BWA index with bwtsw algorithm";
87 fi; 88 bwa index -a bwtsw "${reference_fasta_filename}";
88 fi; 89 fi
89 90 ) &&
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: 91 #else:
104 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 92 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
105 #end if 93 #end if
106 94
107 ## setup vars for rg handling... 95 ## setup vars for rg handling...
132 "${input_type.fastq_input1.forward}" 120 "${input_type.fastq_input1.forward}"
133 #else 121 #else
134 "${input_type.fastq_input1}" 122 "${input_type.fastq_input1}"
135 #end if 123 #end if
136 124
137 > first.sai &amp;&amp; 125 > first.sai &&
138 126
139 bwa aln 127 bwa aln
140 -t "\${GALAXY_SLOTS:-1}" 128 -t "\${GALAXY_SLOTS:-1}"
141 129
142 @command_options@ 130 @command_options@
147 "${input_type.fastq_input1.reverse}" 135 "${input_type.fastq_input1.reverse}"
148 #else 136 #else
149 "${input_type.fastq_input2}" 137 "${input_type.fastq_input2}"
150 #end if 138 #end if
151 139
152 > second.sai &amp;&amp; 140 > second.sai &&
153 141
154 bwa sampe 142 bwa sampe
155 143
156 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True": 144 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True":
157 -a ${$input_type.adv_pe_options.a} 145 -a ${$input_type.adv_pe_options.a}
176 164
177 @command_options@ 165 @command_options@
178 166
179 "${reference_fasta_filename}" 167 "${reference_fasta_filename}"
180 "${input_type.fastq_input1}" 168 "${input_type.fastq_input1}"
181 > first.sai &amp;&amp; 169 > first.sai &&
182 170
183 bwa samse 171 bwa samse
184 172
185 #if str( $input_type.adv_se_options.adv_se_options_selector) == "True": 173 #if str( $input_type.adv_se_options.adv_se_options_selector) == "True":
186 -n ${$input_type.adv_se_options.n} 174 -n ${$input_type.adv_se_options.n}
200 188
201 @command_options@ 189 @command_options@
202 190
203 "${reference_fasta_filename}" 191 "${reference_fasta_filename}"
204 "${input_type.bam_input}" 192 "${input_type.bam_input}"
205 > first.sai &amp;&amp; 193 > first.sai &&
206 194
207 bwa aln 195 bwa aln
208 -t "\${GALAXY_SLOTS:-1}" 196 -t "\${GALAXY_SLOTS:-1}"
209 -b 197 -b
210 -2 198 -2
211 @command_options@ 199 @command_options@
212 "${reference_fasta_filename}" 200 "${reference_fasta_filename}"
213 "${input_type.bam_input}" 201 "${input_type.bam_input}"
214 > second.sai &amp;&amp; 202 > second.sai &&
215 203
216 bwa sampe 204 bwa sampe
217 205
218 #if str( $input_type.adv_bam_pe_options.adv_pe_options_selector) == "True": 206 #if str( $input_type.adv_bam_pe_options.adv_pe_options_selector) == "True":
219 -a ${$input_type.adv_bam_pe_options.a} 207 -a ${$input_type.adv_bam_pe_options.a}
236 224
237 @command_options@ 225 @command_options@
238 226
239 "${reference_fasta_filename}" 227 "${reference_fasta_filename}"
240 "${input_type.bam_input}" 228 "${input_type.bam_input}"
241 > first.sai &amp;&amp; 229 > first.sai &&
242 230
243 bwa samse 231 bwa samse
244 232
245 #if str( $input_type.adv_bam_se_options.adv_se_options_selector) == "True": 233 #if str( $input_type.adv_bam_se_options.adv_se_options_selector) == "True":
246 -n ${$input_type.adv_bam_se_options.n} 234 -n ${$input_type.adv_bam_se_options.n}
249 @read_group_options@ 237 @read_group_options@
250 238
251 "${reference_fasta_filename}" first.sai "${input_type.bam_input}" 239 "${reference_fasta_filename}" first.sai "${input_type.bam_input}"
252 #end if 240 #end if
253 241
254 | samtools view -Sb - > temporary_bam_file.bam &amp;&amp; 242 | samtools view -Sb - > temporary_bam_file.bam &&
255 243
256 samtools sort -f temporary_bam_file.bam ${bam_output} 244 samtools sort -f temporary_bam_file.bam ${bam_output}
245 ]]>
257 </command> 246 </command>
258 247
259 <inputs> 248 <inputs>
260 249
261 <conditional name="reference_source"> 250 <conditional name="reference_source">