Mercurial > repos > bgruening > pharmcat
diff pharmcat.xml @ 1:891283e0ee89 draft default tip
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"
| author | bgruening |
|---|---|
| date | Thu, 05 May 2022 20:27:17 +0000 |
| parents | d67642a21a1d |
| children |
line wrap: on
line diff
--- a/pharmcat.xml Fri Jan 28 21:18:23 2022 +0000 +++ b/pharmcat.xml Thu May 05 20:27:17 2022 +0000 @@ -3,11 +3,11 @@ Pharmacogenomics Clinical Annotation Tool </description> <macros> - <token name="@WRAPPER_VERSION@">1.3.1</token> + <token name="@WRAPPER_VERSION@">1.7.0</token> <token name="@VERSION_SUFFIX@">galaxy0</token> </macros> <requirements> - <container type="docker">pgkb/pharmcat:1.3.1</container> + <container type="docker">pgkb/pharmcat:1.7.0</container> </requirements> <command detect_errors="exit_code"><![CDATA[ ## NAMECALLER FUNCTION @@ -72,14 +72,16 @@ <option value="report">Only reporter</option> </param> <when value="all"> - <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> + <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" + help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> <param name="outside_call" argument="-a" type="data" format="tsv,tabular" label="Gene call TSV file from an outside tool" optional="true"/> <param name="json" argument="-j" type="boolean" truevalue="-j" falsevalue="" label="Output reporter JSON report"/> <param name="phenojson" argument="-pj" type="boolean" truevalue="-pj" falsevalue="" label="Output phenotyper JSON report"/> <!-- <param name="definitions" argument="-na" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> --> </when> <when value="name"> - <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> + <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" + help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> <!-- <param name="definitions" argument="-d" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> --> </when> <when value="pheno"> @@ -89,7 +91,8 @@ <option value="named">Run from the output of the NamedAlleleMatcher</option> </param> <when value="vcf"> - <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> + <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file" + help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/> </when> <when value="named"> <param name="input" argument="-c" type="data" format="json" label="Input json file" help="JSON output of the NamedAlleleCaller pharmcat function"/> @@ -133,8 +136,8 @@ <!-- ALL FUNCTION --> <test expect_num_outputs="3"> <conditional name="function_select"> - <param name="input" ftype="vcf" value="test.vcf"/> - <param name="outside_call" ftype="tabular" value="test.tsv"/> + <param name="input" value="test.vcf" ftype="vcf" /> + <param name="outside_call" value="test.tsv" ftype="tabular"/> <param name="json" value="-j"/> <param name="phenojson" value="-pj"/> </conditional> @@ -158,10 +161,10 @@ <test expect_num_outputs="2"> <conditional name="function_select"> <param name="function" value="name"/> - <param name="input" ftype="vcf" value="test.vcf"/> + <param name="input" value="test.vcf" ftype="vcf"/> </conditional> - <output name="namer_html" file="test_2.html" lines_diff="2"/> - <output name="namer_json" file="test_2.json" lines_diff="2"/> + <output name="namer_html" file="test_2.html" lines_diff="4" ftype="html" /> + <output name="namer_json" file="test_2.json" lines_diff="2" ftype="json" /> </test> <!-- PHENOTYPER FROM VCF WITH OUTSIDE CALLER--> <test expect_num_outputs="1"> @@ -180,18 +183,18 @@ <conditional name="function_select"> <param name="function" value="pheno"/> <conditional name="method"> - <param name="pheno_function" value="named"/> - <param name="input" value="test_2.json"/> + <param name="pheno_function" value="named" /> + <param name="input" value="test_2.json" ftype="json" /> </conditional> </conditional> - <output name="pheno_json" file="test_4.json" lines_diff="1"/> + <output name="pheno_json" file="test_4.json" lines_diff="34"/> </test> <!-- REPORTER --> <test expect_num_outputs="2"> <conditional name="function_select"> + <param name="input" value="test_3.json" ftype="json"/> <param name="function" value="report"/> - <param name="input" value="test_3.json"/> - <param name="text" value="test text"/> + <param name="text" value="test text"/> </conditional> <output name="report_json"> <assert_contents> @@ -215,4 +218,4 @@ <citations> <citation type="doi" >10.1002/cpt.928</citation> </citations> -</tool> \ No newline at end of file +</tool>