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comparison picard_MergeBamAlignment.xml @ 7:08f69add4d06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:36 -0500
parents 2589e6207cb4
children e417b1d6288d
comparison
equal deleted inserted replaced
6:961236c5ec73 7:08f69add4d06
2 <description>merge alignment data with additional info stored in an unmapped BAM dataset</description> 2 <description>merge alignment data with additional info stored in an unmapped BAM dataset</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command> 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 #set $picard_dict = "localref.dict" 9 #set $picard_dict = "localref.dict"
10 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension 10 #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension
11 11
12 ln -s "${reference_source.ref_file}" "${ref_fasta}" &amp;&amp; 12 ln -s "${reference_source.ref_file}" "${ref_fasta}" &&
13 13
14 #if str( $reference_source.reference_source_selector ) == "history": 14 #if str( $reference_source.reference_source_selector ) == "history":
15 15
16 java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" 16 picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
17 QUIET=true 17 QUIET=true
18 VERBOSITY=ERROR 18 VERBOSITY=ERROR
19 19
20 &amp;&amp; 20 &&
21 21
22 #else: 22 #else:
23 23
24 #set $ref_fasta = str( $reference_source.ref_file.fields.path ) 24 #set $ref_fasta = str( $reference_source.ref_file.fields.path )
25 25
26 #end if 26 #end if
27 27
28 java -jar \$JAVA_JAR_PATH/picard.jar 28 picard
29 MergeBamAlignment 29 MergeBamAlignment
30 UNMAPPED_BAM="${unmapped_bam}" 30 UNMAPPED_BAM="${unmapped_bam}"
31 31
32 PAIRED_RUN=true ##This argument is ignored and will be removed. Required. Possible values: {true, false} 32 PAIRED_RUN=true ##This argument is ignored and will be removed. Required. Possible values: {true, false}
33 33
83 83
84 SORT_ORDER=coordinate 84 SORT_ORDER=coordinate
85 QUIET=true 85 QUIET=true
86 VERBOSITY=ERROR 86 VERBOSITY=ERROR
87 87
88 </command> 88 ]]></command>
89 89
90 <inputs> 90 <inputs>
91 91
92 <conditional name="reference_source"> 92 <conditional name="reference_source">
93 <param name="reference_source_selector" type="select" label="Load reference genome from"> 93 <param name="reference_source_selector" type="select" label="Load reference genome from">
192 <param name="aligner_proper_pair_flags" value="False"/> 192 <param name="aligner_proper_pair_flags" value="False"/>
193 <param name="primary_alignment_strategy" value="BestMapq"/> 193 <param name="primary_alignment_strategy" value="BestMapq"/>
194 <param name="clip_overlapping_reads" value="True"/> 194 <param name="clip_overlapping_reads" value="True"/>
195 <param name="include_secondary_alignments" value="True"/> 195 <param name="include_secondary_alignments" value="True"/>
196 <param name="add_mate_cigar" value="True"/> 196 <param name="add_mate_cigar" value="True"/>
197 <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="2"/> 197 <output name="outFile" file="picard_MergeBamAlignment_test1.bam" ftype="bam" lines_diff="4"/>
198 </test> 198 </test>
199 </tests> 199 </tests>
200 200
201 <stdio>
202 <exit_code range="1:" level="fatal"/>
203 </stdio>
204 201
205 <help> 202 <help>
206 203
207 .. class:: infomark 204 .. class:: infomark
208 205