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comparison sam_merge.xml @ 1:1f18d80df2a5 draft

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author devteam
date Wed, 11 Feb 2015 17:41:13 -0500
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0:a7a49d31c5cf 1:1f18d80df2a5
1 <tool id="sam_merge2" name="Merge BAM Files" version="1.1.2"> 1 <tool id="sam_merge2" name="Merge BAM Files" version="1.2.0">
2 <description>merges BAM files together</description> 2 <description>merges BAM files together</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.56.0">picard</requirement> 4 <requirement type="package" version="1.56.0">picard</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <stdio>
7 java -Xmx2G -jar \$JAVA_JAR_PATH/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 TMP_DIR=$__new_file_path__ 7 <exit_code range="1:" />
8 #for $i in $inputs 8 <exit_code range=":-1" />
9 I=${i.input} 9 <regex match="Error:" />
10 #end for 10 <regex match="Exception:" />
11 2&gt; $outlog 11 </stdio>
12 || echo "Error running Picard MergeSamFiles" >&amp;2 12 <command>
13 </command> 13 <![CDATA[
14 <inputs> 14 java -Xmx2G
15 <param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam" 15 -jar \$JAVA_JAR_PATH/MergeSamFiles.jar
16 help="This name will appear in your history so use it to remember what the new file in your history contains" /> 16 MSD=$mergeSD
17 <param name="mergeSD" value="true" type="boolean" label="Merge all component bam file headers into the merged bam file" 17 VALIDATION_STRINGENCY=LENIENT
18 truevalue="true" falsevalue="false" checked="yes" 18 O="$output1"
19 help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" /> 19 TMP_DIR=$__new_file_path__
20 <param name="input1" label="First file" type="data" format="bam,sam" /> 20 #for $input in $inputs
21 <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." /> 21 I="${input}"
22 <repeat name="inputs" title="Input Files"> 22 #end for
23 <param name="input" label="Add file" type="data" format="bam,sam" /> 23 ]]>
24 </repeat> 24 </command>
25 </inputs> 25 <inputs>
26 <outputs> 26 <param name="inputs" type="data" format="bam,sam" multiple="True" label="Files to merge" />
27 <data format="bam" name="output1" label="${title}.bam" /> 27 <param name="mergeSD" type="boolean" label="Merge all component bam file headers into the merged bam file"
28 <data format="txt" name="outlog" label="${title}_${tool.name}.log" /> 28 truevalue="true" falsevalue="false" checked="yes"
29 </outputs> 29 help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" />
30 <tests> 30 </inputs>
31 <!-- TODO: add ability to test framework to test without at least 31 <outputs>
32 one repeat element value 32 <data format="bam" name="output1" />
33 --> 33 </outputs>
34 <test> 34 <tests>
35 <param name="title" value="test1" /> 35 <test>
36 <param name="mergeSD" value="true" /> 36 <param name="mergeSD" value="true" />
37 <param name="input1" value="sam_merge_in1.bam" ftype="bam" /> 37 <param name="inputs" value="sam_merge_in1.bam,sam_merge_in2.bam" ftype="bam" />
38 <param name="input2" value="sam_merge_in2.bam" ftype="bam" /> 38 <output name="output1" file="sam_merge_out1.bam" ftype="bam" />
39 <output name="output1" file="sam_merge_out1.bam" ftype="bam" /> 39 </test>
40 <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="11"/> 40 <test>
41 </test> 41 <param name="mergeSD" value="true" />
42 <test> 42 <param name="inputs" value="sam_merge_in1.bam,sam_merge_in2.bam,sam_merge_in3.bam" ftype="bam" />
43 <param name="title" value="test2" /> 43 <output name="output1" file="sam_merge_out2.bam" ftype="bam" />
44 <param name="mergeSD" value="true" /> 44 </test>
45 <param name="input1" value="sam_merge_in1.bam" ftype="bam" />
46 <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
47 <param name="input" value="sam_merge_in3.bam" ftype="bam" />
48 <output name="output1" file="sam_merge_out2.bam" ftype="bam" />
49 <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="11"/>
50 </test>
51 </tests> 45 </tests>
52 <help> 46 <help>
53 47 <![CDATA[
54 **What it does** 48 **What it does**
55 49
56 This tool uses the Picard_ merge command to merge any number of BAM files together into one BAM file while preserving the BAM 50 This tool uses the Picard_ merge command to merge any number of BAM files together into one BAM file while preserving the BAM
57 metadata such as read groups 51 metadata such as read groups.
58 52
59 .. _Picard: http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles 53 .. _Picard: http://broadinstitute.github.io/picard/
60 54 ]]>
61 </help> 55 </help>
62 </tool> 56 </tool>