| Previous changeset 2:cf06b44624c7 (2019-02-21) Next changeset 4:256e65e460b7 (2019-06-05) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a |
|
modified:
bcftools_mpileup.xml |
| b |
| diff -r cf06b44624c7 -r 4e1d23e5c691 bcftools_mpileup.xml --- a/bcftools_mpileup.xml Thu Feb 21 16:09:57 2019 -0500 +++ b/bcftools_mpileup.xml Mon May 27 14:23:55 2019 -0400 |
| b |
| @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1"> <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description> <macros> <token name="@EXECUTABLE@">mpileup</token> @@ -246,11 +246,12 @@ <option value="adjust">Set base and mapping quality options</option> </param> <when value="adjust"> - <param name="baq" type="select" optional="true" label="per-Base Alignment Quality"> + <param name="baq" type="select" label="per-Base Alignment Quality"> <help> --no-BAQ; BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments. --redo-BAQ; ignore existing BQ tags </help> + <option value="">Default</option> <option value="--no-BAQ">disable BAQ (per-Base Alignment Quality) (no-BAQ)</option> <option value="--redo-BAQ">recalculate BAQ on the fly, ignore existing BQs (redo-BAQ)</option> </param> @@ -344,6 +345,22 @@ </test> <test> <param name="input_number" value="single" /> + <param name="input_bam" ftype="bam" value="mpileup.1.bam" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> + <param name="quality_settings" value="adjust" /> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + <has_text text="mpileup" /> + <has_text text="HG00100" /> + <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;" /> + <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;" /> + </assert_contents> + </output> + </test> + <test> + <param name="input_number" value="single" /> <param name="input_bam" ftype="cram" value="mpileup.3.cram" /> <param name="reference_source_selector" value="history" /> <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> |