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comparison picard_CollectAlignmentSummaryMetrics.xml @ 8:3a3234d7a2e8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:53:10 -0400
parents 3d4f1fa26f0e
children 5eaa8a968300
comparison
equal deleted inserted replaced
7:379fdf4c41ac 8:3a3234d7a2e8
1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="1.126.0"> 1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.0">
2 <description>writes a file containing summary alignment metrics</description> 2 <description>writes a file containing summary alignment metrics</description>
3 <requirements>
4 <requirement type="package" version="1.126.0">picard</requirement>
5 </requirements>
6
7 <macros> 3 <macros>
8 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
9 </macros> 5 </macros>
10 6 <expand macro="requirements" />
11 <command> 7 <command>
12 @java_options@ 8 @java_options@
13 ##set up input files 9 ##set up input files
14 10
15 #set $reference_fasta_filename = "localref.fa" 11 #set $reference_fasta_filename = "localref.fa"
53 </options> 49 </options>
54 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 50 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
55 </param> 51 </param>
56 </when> 52 </when>
57 <when value="history"> 53 <when value="history">
58 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> 54 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
59 </when> 55 </when>
60 </conditional> 56 </conditional>
61 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL"> 57 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
62 <option value="ALL_READS" selected="True">All reads</option> 58 <option value="ALL_READS" selected="True">All reads</option>
63 <option value="SAMPLE">Sample</option> 59 <option value="SAMPLE">Sample</option>