Mercurial > repos > iuc > bcftools_plugin_tag2tag
diff bcftools_plugin_tag2tag.xml @ 5:114d43c4a41f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
| author | iuc |
|---|---|
| date | Thu, 13 Apr 2017 17:42:36 -0400 |
| parents | 09533c5972fb |
| children | 6cbb9c47795c |
line wrap: on
line diff
--- a/bcftools_plugin_tag2tag.xml Sat Mar 11 18:03:30 2017 -0500 +++ b/bcftools_plugin_tag2tag.xml Thu Apr 13 17:42:36 2017 -0400 @@ -13,6 +13,7 @@ @PREPARE_INPUT_FILE@ #set $section = $sec_restrict @PREPARE_TARGETS_FILE@ +@PREPARE_REGIONS_FILE@ bcftools plugin @EXECUTABLE@ @@ -34,7 +35,10 @@ -- ${section.conversion} ${section.replace} -> "$output_file" +#if $section.conversion == '--gp-to-gt' and float($section.threshold) is not None: + --threshold ${section.threshold} +#end if +> '$output_file' ]]> </command> <inputs> @@ -48,9 +52,12 @@ <section name="sec_plugin" expanded="true" title="Plugin Options"> <param name="conversion" type="select" label="Tag conversion"> <option value="--gp-to-gl" selected="true">convert FORMAT/GP to FORMAT/GL</option> + <option value="--gp-to-gt" selected="true">convert FORMAT/GP to FORMAT/GT (by taking argmax of GP)</option> <option value="--gl-to-pl">convert FORMAT/GL to FORMAT/PL</option> + <option value="--pl-to-gl">convert FORMAT/PL to FORMAT/GL</option> </param> <param name="replace" type="boolean" truevalue="--replace" falsevalue="" checked="true" label="drop the source tag" help="(\-\-replace)" /> + <param name="" type="float" value=".1" min="0." max="1.0" optional="true" label="threshold for GP to GT hard-call" help="(\-\-threshold float)" /> </section> <expand macro="macro_select_output_type" /> </inputs> @@ -61,10 +68,11 @@ <test> <param name="input_file" ftype="vcf" value="view.GL.vcf" /> <param name="replace" value="True" /> - <param name="conversion" value="--gp-to-gl" /> + <param name="conversion" value="--gl-to-pl" /> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> + <has_text text="ID=PL,"/> </assert_contents> </output> </test>