Mercurial > repos > iuc > beagle
changeset 1:d0a6954d0a0a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit 665be55fed0fde169c24f17dd2867b2257b638d8
| author | iuc |
|---|---|
| date | Sun, 22 Jan 2023 12:42:30 +0000 |
| parents | 117d42db0a30 |
| children | |
| files | beagle.xml macros.xml |
| diffstat | 2 files changed, 24 insertions(+), 17 deletions(-) [+] |
line wrap: on
line diff
--- a/beagle.xml Sat Jul 03 23:33:08 2021 +0000 +++ b/beagle.xml Sun Jan 22 12:42:30 2023 +0000 @@ -7,15 +7,14 @@ <expand macro='requirements' /> <command detect_errors='exit_code'><![CDATA[ #set out_prefix='out' - #if $optional_inputs.ref.ext == 'bref3' - ln -s '${optional_inputs.ref}' ref.bref3 && + #if $optional_inputs.ref + ln -s '${optional_inputs.ref}' ref.$optional_inputs.ref.ext && #end if + beagle gt='${gt}' - #if $optional_inputs.ref and $optional_inputs.ref.ext == 'bref3' - ref=ref.bref3 - #else if $optional_inputs.ref - ref='${optional_inputs.ref}' + #if $optional_inputs.ref + ref=ref.$optional_inputs.ref.ext #end if #if $optional_inputs.map map='${optional_inputs.map}' @@ -146,7 +145,7 @@ <tests> <!-- Test default values --> <test expect_num_outputs="2"> - <param name="gt" value="test.vcf.gz"/> + <param name="gt" value="test.vcf.gz" ftype="vcf"/> <param name="chrom" value="22:100-"/> <param name="ne" value="1000000"/> <param name="window" value="40.0"/> @@ -160,11 +159,15 @@ <param name="phase_states" value="280"/> </section> <output name="vcf_file" file="test_output.vcf" ftype="vcf" lines_diff="3"/> - <output name="log_file" file="test_output.log" ftype="txt" lines_diff="16"/> + <output name="log_file" file="test_output.log" ftype="txt" lines_diff="16"> + <assert_contents> + <has_text text="WARNING" negate="true"/> + </assert_contents> + </output> </test> <!-- Test plink file--> <test expect_num_outputs="2"> - <param name="gt" value="test.vcf.gz"/> + <param name="gt" value="test.vcf.gz" ftype="vcf"/> <param name="ne" value="1000000"/> <param name="window" value="30.0"/> <param name="overlap" value="3.0"/> @@ -186,19 +189,21 @@ <output name="log_file" ftype="txt"> <assert_contents> <has_text text="Reference markers: 223"/> - <has_size value="1586" delta="10"/> + <has_size value="1586" delta="100"/> + <has_text text="WARNING" negate="true"/> + <has_text_matching expression="beagle.*jar finished"/> </assert_contents> </output> </test> <!-- Test ref VCF input --> <test expect_num_outputs="2"> - <param name="gt" value="target.vcf.gz"/> + <param name="gt" value="target.vcf.gz" ftype="vcf"/> <param name="ne" value="1000000"/> <param name="window" value="40.0"/> <param name="overlap" value="2.0"/> <param name="output_log" value="true"/> <section name="optional_inputs"> - <param name="ref" value="ref.vcf.gz"/> + <param name="ref" value="ref.vcf.gz" ftype="vcf"/> </section> <section name="imputation_parameters"> <param name="impute" value="true"/> @@ -218,18 +223,20 @@ <output name="log_file" ftype="txt"> <assert_contents> <has_text text="Reference markers: 223"/> - <has_size value="1801" delta="10"/> + <has_size value="1600" delta="100"/> + <has_text text="WARNING" negate="true"/> + <has_text_matching expression="beagle.*jar finished"/> </assert_contents> </output> </test> <!-- Test ref bref3 input --> <test expect_num_outputs="1"> - <param name="gt" value="target.vcf.gz"/> + <param name="gt" value="target.vcf.gz" ftype="vcf"/> <param name="ne" value="1000000"/> <param name="window" value="40.0"/> <param name="overlap" value="2.0"/> <section name="optional_inputs"> - <param name="ref" value="ref.bref3"/> + <param name="ref" value="ref.bref3" ftype="bref3"/> </section> <section name="imputation_parameters"> <param name="impute" value="true"/> @@ -269,7 +276,7 @@ **HapMap genetic maps** HapMap genetic maps in PLINK format for GRCh36, GRCh37, and GRCh38 are available -in `this link <http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/>`_ +in `this links <https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/>`_ ----
--- a/macros.xml Sat Jul 03 23:33:08 2021 +0000 +++ b/macros.xml Sun Jan 22 12:42:30 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">5.2_21Apr21.304</token> - <token name="@SUFFIX_VERSION@">0</token> + <token name="@SUFFIX_VERSION@">1</token> <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0196</edam_topic>