Mercurial > repos > iuc > merquryfk_hapmaker
changeset 3:fe77aa22ae94 draft default tip
planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit f02f3754424a68a1463fa75e9523d49e60d68373
| author | iuc |
|---|---|
| date | Wed, 05 Mar 2025 19:07:16 +0000 |
| parents | e9725214ab38 |
| children | |
| files | hapmaker.xml test-data/HapK_ktab_files.tar.gz test-data/maternal.hap.ktab test-data/paternal.hap.ktab |
| diffstat | 4 files changed, 21 insertions(+), 13 deletions(-) [+] |
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--- a/hapmaker.xml Tue Feb 25 13:34:53 2025 +0000 +++ b/hapmaker.xml Wed Mar 05 19:07:16 2025 +0000 @@ -11,19 +11,19 @@ && tar -xf maternal.tar && mv ktabfiles ktabfiles_maternal && mv ktabfiles_maternal/output.ktab input_files/maternal.ktab - && mv "\$(find ktabfiles_maternal -type f -name '*.ktab.1')" "input_files/.maternal.ktab.1" + && mv ktabfiles_maternal/.*.ktab* input_files/.maternal.ktab.1 && ln -s '$paternal_ktab_tar' paternal.tar && tar -xf paternal.tar && mv ktabfiles ktabfiles_paternal && mv ktabfiles_paternal/output.ktab input_files/paternal.ktab - && mv "\$(find ktabfiles_paternal -type f -name '*.ktab.1')" "input_files/.paternal.ktab.1" + && mv ktabfiles_paternal/.*.ktab* input_files/.paternal.ktab.1 && ln -s '$child_ktab_tar' child.tar && tar -xf child.tar && mv ktabfiles ktabfiles_child && mv ktabfiles_child/output.ktab input_files/child.ktab - && mv "\$(find ktabfiles_child -type f -name '*.ktab.1')" "input_files/.child.ktab.1" + && mv ktabfiles_child/.*.ktab* input_files/.child.ktab.1 && HAPmaker -v - -T\${GALAXY_SLOTS:-4} + -T\${GALAXY_SLOTS:-1} input_files/maternal.ktab input_files/paternal.ktab input_files/child.ktab @@ -36,22 +36,30 @@ <param name="child_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of child ktab file from FastK"/> </inputs> <outputs> - <data name="paternal_out" format="fastk_ktab" from_work_dir="paternal.hap.ktab" label="${tool.name} on ${on_string}: paternal hap-mers"/> - <data name="maternal_out" format="fastk_ktab" from_work_dir="maternal.hap.ktab" label="${tool.name} on ${on_string}: maternal hap-mers"/> + <data name="paternal_out" format="fastk_ktab" from_work_dir="input_files/paternal.hap.ktab" label="${tool.name} on ${on_string}: paternal hap-mers"/> + <data name="maternal_out" format="fastk_ktab" from_work_dir="input_files/maternal.hap.ktab" label="${tool.name} on ${on_string}: maternal hap-mers"/> <data name="intermediate_ktab" format="fastk_ktab_tar" from_work_dir="HapK_ktab_files.tar.gz" label="${tool.name} on ${on_string}: HapMaker Intermediate Ktab files"/> </outputs> <tests> <test expect_num_outputs="3"> - <param name="maternal_ktab_tar" ftype="fastk_ktab_tar" value="maternal.tar"/> - <param name="paternal_ktab_tar" ftype="fastk_ktab_tar" value="paternal.tar"/> - <param name="child_ktab_tar" ftype="fastk_ktab_tar" value="child.tar"/> - <output name="paternal_out" value="paternal.hap.ktab"/> - <output name="maternal_out" value="maternal.hap.ktab"/> + <param name="maternal_ktab_tar" ftype="fastk_ktab_tar" location="https://zenodo.org/records/14965629/files/maternal.fastk_ktab_tar"/> + <param name="paternal_ktab_tar" ftype="fastk_ktab_tar" location="https://zenodo.org/records/14965629/files/paternal.fastk_ktab_tar"/> + <param name="child_ktab_tar" ftype="fastk_ktab_tar" location="https://zenodo.org/records/14965629/files/child.fastk_ktab_tar"/> + <output name="paternal_out" ftype="fastk_ktab"> + <assert_contents> + <has_size value="524304" delta="2000"/> + </assert_contents> + </output> + <output name="maternal_out" ftype="fastk_ktab"> + <assert_contents> + <has_size value="524304" delta="2000"/> + </assert_contents> + </output> <output name="intermediate_ktab" ftype="fastk_ktab_tar"> - <assert_contents> + <assert_contents> <has_archive_member path="hapmaker_ktabs/.maternal.hap.ktab.1"/> <has_archive_member path="hapmaker_ktabs/.paternal.hap.ktab.1"/> - </assert_contents> + </assert_contents> </output> </test> </tests>