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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2 |
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modified:
lofreq_call.xml |
| b |
| diff -r e1461b5c52a0 -r 4805fe3d8fda lofreq_call.xml --- a/lofreq_call.xml Mon Oct 05 20:14:06 2020 +0000 +++ b/lofreq_call.xml Wed Jul 06 09:25:57 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy1" profile="18.01"> +<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy2" profile="18.01"> <description>with LoFreq</description> <macros> <import>macros.xml</import> @@ -103,6 +103,7 @@ && gzip -df variants.vcf.gz #end if #end if + && echo $filter_control.filter_type ]]></command> <inputs> <param type="data" name="reads" format="bam" label="Input reads in BAM format" /> @@ -285,7 +286,13 @@ <param name="reads" ftype="bam" value="lofreq-in1.bam" /> <param name="ref_selector" value="history" /> <param name="ref" ftype="fasta" value="pBR322.fa" /> - <output name="variants" file="call-out1.vcf" lines_diff="4" /> + <!-- lines_diff="4" should be sufficient, but https://github.com/CSB5/lofreq/issues/131 --> + <output name="variants" file="call-out1.vcf" lines_diff="6" /> + <assert_command> + <has_text text="--sig 0.01"/> + <has_text text="--bonf dynamic"/> + <has_text text="--no-default-filter" negate="true"/> + </assert_command> </test> <test> <param name="reads" ftype="bam" value="lofreq-in1.bam" /> @@ -294,7 +301,8 @@ <conditional name="call_control"> <param name="set_call_options" value="yes" /> </conditional> - <output name="variants" file="call-out1.vcf" lines_diff="4" /> + <!-- lines_diff="4" should be sufficient, but https://github.com/CSB5/lofreq/issues/131 --> + <output name="variants" file="call-out1.vcf" lines_diff="6" /> </test> <test> <param name="reads" ftype="bam" value="lofreq-in1.bam" /> @@ -310,7 +318,8 @@ </conditional> </section> </conditional> - <output name="variants" file="call-out1.vcf" lines_diff="4" /> + <!-- lines_diff="4" should be sufficient, but https://github.com/CSB5/lofreq/issues/131 --> + <output name="variants" file="call-out1.vcf" lines_diff="6" /> </test> <test> <param name="reads" ftype="bam" value="lofreq-in1.bam" /> |