| Previous changeset 9:5eaa8a968300 (2015-10-09) Next changeset 11:efc56ee1ade4 (2015-11-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 |
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modified:
picard_CollectAlignmentSummaryMetrics.xml |
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| diff -r 5eaa8a968300 -r 777ccdd1d6e4 picard_CollectAlignmentSummaryMetrics.xml --- a/picard_CollectAlignmentSummaryMetrics.xml Fri Oct 09 17:43:13 2015 -0400 +++ b/picard_CollectAlignmentSummaryMetrics.xml Sun Oct 11 10:46:17 2015 -0400 |
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| @@ -1,21 +1,24 @@ -<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.0"> +<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.1"> <description>writes a file containing summary alignment metrics</description> <macros> <import>picard_macros.xml</import> </macros> <expand macro="requirements" /> + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> <command> @java_options@ ##set up input files #set $reference_fasta_filename = "localref.fa" - + #if str( $reference_source.reference_source_selector ) == "history": ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && #else: #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) #end if - + java -jar \$JAVA_JAR_PATH/picard.jar CollectAlignmentSummaryMetrics INPUT="${inputFile}" @@ -24,11 +27,13 @@ #for $sequence in $adapters: ADAPTER_SEQUENCE="${sequence.adapter}" #end for - METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" + #for $level in str($metric_accumulation_level).split(','): + METRIC_ACCUMULATION_LEVEL="${level}" + #end for IS_BISULFITE_SEQUENCED="${bisulphite}" - + REFERENCE_SEQUENCE="${reference_fasta_filename}" - + ASSUME_SORTED="${assume_sorted}" VALIDATION_STRINGENCY="${validation_stringency}" @@ -66,20 +71,12 @@ <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/> </repeat> <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/> - <expand macro="VS" /> - + </inputs> - <outputs> <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> </outputs> - - <stdio> - <exit_code range="1:" level="fatal"/> - </stdio> - - <tests> <test> <param name="bisulphite" value="false" /> @@ -92,7 +89,6 @@ <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/> </test> </tests> - <help> .. class:: infomark |