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comparison bowtie2_wrapper.xml @ 4:1fc845afa3ac draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 32fe80982b5c59687eece667f0372002588566f8-dirty
author devteam
date Tue, 21 Jul 2015 13:00:51 -0400
parents ceb6467e276c
children 42bb952b4e3c
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3:ceb6467e276c 4:1fc845afa3ac
1 <tool id="bowtie2" name="Bowtie2" version="0.4"> 1 <tool id="bowtie2" name="Bowtie2" version="0.5">
2 <!-- Wrapper compatible with Bowtie version 2.2.4 --> 2 <!-- Wrapper compatible with Bowtie version 2.2.4 -->
3 <description>- map reads against reference genome</description> 3 <description>- map reads against reference genome</description>
4 <version_command>bowtie2 --version</version_command> 4 <version_command>bowtie2 --version</version_command>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="2.2.4">bowtie2</requirement> 6 <requirement type="package" version="2.2.4">bowtie2</requirement>
143 --seed "${analysis_type.other_options.seed}" 143 --seed "${analysis_type.other_options.seed}"
144 #end if 144 #end if
145 145
146 #elif str( $analysis_type.analysis_type_selector ) == "cline": 146 #elif str( $analysis_type.analysis_type_selector ) == "cline":
147 ${analysis_type.cline} 147 ${analysis_type.cline}
148 #end if 148 #end if
149 149
150 -S "galaxy_bowtie_2_output.sam" &amp;&amp;
151
150 ## view/sort and output BAM file 152 ## view/sort and output BAM file
151 | samtools view -Su - | samtools sort -o - - > $output 153 ( samtools view -Su "galaxy_bowtie_2_output.sam" | samtools sort -o - - > $output )
152 154
153 ## rename unaligned sequence files 155 ## rename unaligned sequence files
154 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: 156 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
155 #set left = str($output_unaligned_reads_l).replace( '.dat', '.1.dat' ) 157 #from os.path import splitext
156 #set right = str($output_unaligned_reads_l).replace( '.dat', '.2.dat' ) 158 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
157 159 &amp;&amp; mv "${ _unaligned_root }.1${_unaligned_ext}" "${ output_unaligned_reads_l }"
158 ; mv $left $output_unaligned_reads_l; 160 &amp;&amp; mv "${ _unaligned_root }.2${_unaligned_ext}" "${ output_unaligned_reads_r }"
159 mv $right $output_unaligned_reads_r
160 #end if 161 #end if
161 162
162 </command> 163 </command>
163 164
164 <!-- basic error handling --> 165 <!-- basic error handling -->