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comparison picard_CollectAlignmentSummaryMetrics.xml @ 31:585027e65f3b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 70d2a66c405be58d4413753792bcadf212a4da84
author iuc
date Sat, 25 Feb 2023 20:33:49 +0000
parents 2a17c789e0a5
children f9242e01365a
comparison
equal deleted inserted replaced
30:b502c227b5e6 31:585027e65f3b
1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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 <token name="@WRAPPER_VERSION@">1</token> 5 <token name="@WRAPPER_VERSION@">2</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @java_options@ 9 @java_options@
10 @symlink_element_identifier@ 10 @symlink_element_identifier@
69 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/> 69 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/>
70 <expand macro="VS" /> 70 <expand macro="VS" />
71 71
72 </inputs> 72 </inputs>
73 <outputs> 73 <outputs>
74 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> 74 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: tablular"/>
75 </outputs> 75 </outputs>
76 <tests> 76 <tests>
77 <test> 77 <test>
78 <param name="bisulphite" value="false" /> 78 <param name="bisulphite" value="false" />
79 <param name="sorted" value="true" /> 79 <param name="assume_sorted" value="true" />
80 <param name="adaptors" value="" /> 80 <repeat name="adapters">
81 <param name="adapter" value = ""/>
82 </repeat>
81 <param name="maxinsert" value="100000" /> 83 <param name="maxinsert" value="100000" />
82 <param name="reference_source_selector" value="history" /> 84 <param name="reference_source_selector" value="history" />
83 <param name="ref_file" value="picard_CASM_ref.fa" /> 85 <param name="ref_file" value="picard_CASM_ref.fa" />
84 <param name="inputFile" value="picard_CASM.bam" ftype="bam" /> 86 <param name="inputFile" value="picard_CASM.bam" ftype="bam" />
85 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/> 87 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>