Mercurial > repos > iuc > bcftools_plugin_mendelian
diff bcftools_plugin_mendelian.xml @ 5:8fa5f4cf9797 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
| author | iuc |
|---|---|
| date | Thu, 13 Apr 2017 16:21:48 -0400 |
| parents | 0e2e495eec58 |
| children | fa3a07122ac9 |
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--- a/bcftools_plugin_mendelian.xml Sat Mar 11 17:54:18 2017 -0500 +++ b/bcftools_plugin_mendelian.xml Thu Apr 13 16:21:48 2017 -0400 @@ -13,6 +13,7 @@ @PREPARE_INPUT_FILE@ #set $section = $sec_restrict @PREPARE_TARGETS_FILE@ +@PREPARE_REGIONS_FILE@ bcftools plugin @EXECUTABLE@ @@ -53,7 +54,7 @@ #end if #end if 2> tmp_stderr -> "$output_file" +> '$output_file' && cat tmp_stderr ]]> </command> @@ -84,8 +85,8 @@ <param name="mode" type="select" label="Action" multiple="true" min="1"> <option value="count">count the number of consistent sites</option> <option value="delete">delete inconsistent genotypes (set to './.')</option> - <option value="+">consistent sites (+)</option> - <option value="x">inconsistent sites (x)</option> + <option value="+">list consistent sites (+)</option> + <option value="x">list inconsistent sites (x)</option> </param> </section> <expand macro="macro_select_output_type" /> @@ -105,8 +106,8 @@ <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> - <has_text text="2698758" /> - <not_has_text text="2698769" /> + <has_text text="mendelian" /> + <has_text_matching expression="X\t2698769\t.\tAAG\tA\t999\t.\t.\tGT:PL:GP\t./."/> </assert_contents> </output> </test> @@ -121,6 +122,7 @@ <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> + <has_text text="mendelian" /> <not_has_text text="2698758" /> <has_text text="2698769" /> </assert_contents>