| Previous changeset 10:07d55d9ea9a4 (2013-12-16) Next changeset 12:aaf568580946 (2014-06-20) |
|
Commit message:
Check exit code instead of stderr, since FreeBayes writes warnings there (e.g. "Could not find any mapped reads in target region chr1:955302..955952"). Also document change of available options in FreeBayes >= 0.9.9. |
|
modified:
freebayes.xml |
| b |
| diff -r 07d55d9ea9a4 -r e9ebed0c12f6 freebayes.xml --- a/freebayes.xml Mon Dec 16 16:31:57 2013 -0500 +++ b/freebayes.xml Mon Feb 17 10:53:56 2014 -0500 |
| b |
| @@ -156,7 +156,6 @@ --read-dependence-factor "${options_type.section_algorithmic_features_type.read_dependence_factor}" ${options_type.section_algorithmic_features_type.no_marginals} #end if - #end if </command> <inputs> @@ -169,7 +168,7 @@ <repeat name="input_bams" title="Sample BAM file" min="1"> <param name="input_bam" type="data" format="bam" label="BAM file"> <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> + <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> </param> </repeat> <param name="ref_file" type="select" label="Using reference genome"> @@ -307,7 +306,9 @@ </conditional> <!-- indel realignment --> - <param name="left_align_indels" type="boolean" truevalue="--left-align-indels" falsevalue="" checked="False" label="Left-realign and merge gaps embedded in reads" /> + <!-- in FreeBayes < 0.9.9 the default is to not left-align indels and the available option is - -left-align-indels, + in FreeBayes >= 0.9.9 the default is to left-align indels and the available option is - -dont-left-align-indels --> + <param name="left_align_indels" type="boolean" truevalue="--left-align-indels" falsevalue="" checked="False" label="Left align indels" /> <!-- input filters --> <conditional name="section_input_filters_type"> @@ -429,6 +430,9 @@ <output name="output_vcf" file="freebayes_out_1.vcf.contains" compare="contains"/> </test> </tests> + <stdio> + <exit_code range="1:" /> + </stdio> <help> **What it does** |