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comparison picard_CollectAlignmentSummaryMetrics.xml @ 4:2589e6207cb4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:27:49 -0400
parents 52fdfc45590a
children 08f69add4d06
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3:52fdfc45590a 4:2589e6207cb4
1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.0"> 1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.1">
2 <description>writes a file containing summary alignment metrics</description> 2 <description>writes a file containing summary alignment metrics</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 <stdio>
8 <exit_code range="1:" level="fatal"/>
9 </stdio>
7 <command> 10 <command>
8 @java_options@ 11 @java_options@
9 ##set up input files 12 ##set up input files
10 13
11 #set $reference_fasta_filename = "localref.fa" 14 #set $reference_fasta_filename = "localref.fa"
12 15
13 #if str( $reference_source.reference_source_selector ) == "history": 16 #if str( $reference_source.reference_source_selector ) == "history":
14 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp; 17 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
15 #else: 18 #else:
16 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
17 #end if 20 #end if
18 21
19 java -jar \$JAVA_JAR_PATH/picard.jar 22 java -jar \$JAVA_JAR_PATH/picard.jar
20 CollectAlignmentSummaryMetrics 23 CollectAlignmentSummaryMetrics
21 INPUT="${inputFile}" 24 INPUT="${inputFile}"
22 OUTPUT="${outFile}" 25 OUTPUT="${outFile}"
23 MAX_INSERT_SIZE=${maxinsert} 26 MAX_INSERT_SIZE=${maxinsert}
24 #for $sequence in $adapters: 27 #for $sequence in $adapters:
25 ADAPTER_SEQUENCE="${sequence.adapter}" 28 ADAPTER_SEQUENCE="${sequence.adapter}"
26 #end for 29 #end for
27 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" 30 #for $level in str($metric_accumulation_level).split(','):
31 METRIC_ACCUMULATION_LEVEL="${level}"
32 #end for
28 IS_BISULFITE_SEQUENCED="${bisulphite}" 33 IS_BISULFITE_SEQUENCED="${bisulphite}"
29 34
30 REFERENCE_SEQUENCE="${reference_fasta_filename}" 35 REFERENCE_SEQUENCE="${reference_fasta_filename}"
31 36
32 ASSUME_SORTED="${assume_sorted}" 37 ASSUME_SORTED="${assume_sorted}"
33 38
34 VALIDATION_STRINGENCY="${validation_stringency}" 39 VALIDATION_STRINGENCY="${validation_stringency}"
35 QUIET=true 40 QUIET=true
36 VERBOSITY=ERROR 41 VERBOSITY=ERROR
61 <option value="READ_GROUP">Read group</option> 66 <option value="READ_GROUP">Read group</option>
62 </param> 67 </param>
63 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> 68 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
64 <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/> 69 <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/>
65 <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences"> 70 <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences">
66 <param name="adapter" type="text" size="50" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/> 71 <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
67 </repeat> 72 </repeat>
68 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" size="20" help="MAX_INSERT_SIZE"/> 73 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/>
69
70 <expand macro="VS" /> 74 <expand macro="VS" />
71 75
72 </inputs> 76 </inputs>
73
74 <outputs> 77 <outputs>
75 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> 78 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
76 </outputs> 79 </outputs>
77
78 <stdio>
79 <exit_code range="1:" level="fatal"/>
80 </stdio>
81
82
83 <tests> 80 <tests>
84 <test> 81 <test>
85 <param name="bisulphite" value="false" /> 82 <param name="bisulphite" value="false" />
86 <param name="sorted" value="true" /> 83 <param name="sorted" value="true" />
87 <param name="adaptors" value="" /> 84 <param name="adaptors" value="" />
90 <param name="ref_file" value="picard_CASM_ref.fa" /> 87 <param name="ref_file" value="picard_CASM_ref.fa" />
91 <param name="inputFile" value="picard_CASM.bam" ftype="bam" /> 88 <param name="inputFile" value="picard_CASM.bam" ftype="bam" />
92 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/> 89 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>
93 </test> 90 </test>
94 </tests> 91 </tests>
95
96 <help> 92 <help>
97 93
98 .. class:: infomark 94 .. class:: infomark
99 95
100 **Purpose** 96 **Purpose**