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comparison hapmaker.xml @ 3:3ec2cd53b675 draft default tip

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planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit f02f3754424a68a1463fa75e9523d49e60d68373
author iuc
date Wed, 05 Mar 2025 19:06:33 +0000
parents 5eb60882a2a8
children
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2:2fbd93fe4a6f 3:3ec2cd53b675
9 && mkdir -p hapmaker_ktabs 9 && mkdir -p hapmaker_ktabs
10 && ln -s '$maternal_ktab_tar' maternal.tar 10 && ln -s '$maternal_ktab_tar' maternal.tar
11 && tar -xf maternal.tar 11 && tar -xf maternal.tar
12 && mv ktabfiles ktabfiles_maternal 12 && mv ktabfiles ktabfiles_maternal
13 && mv ktabfiles_maternal/output.ktab input_files/maternal.ktab 13 && mv ktabfiles_maternal/output.ktab input_files/maternal.ktab
14 && mv "\$(find ktabfiles_maternal -type f -name '*.ktab.1')" "input_files/.maternal.ktab.1" 14 && mv ktabfiles_maternal/.*.ktab* input_files/.maternal.ktab.1
15 && ln -s '$paternal_ktab_tar' paternal.tar 15 && ln -s '$paternal_ktab_tar' paternal.tar
16 && tar -xf paternal.tar 16 && tar -xf paternal.tar
17 && mv ktabfiles ktabfiles_paternal 17 && mv ktabfiles ktabfiles_paternal
18 && mv ktabfiles_paternal/output.ktab input_files/paternal.ktab 18 && mv ktabfiles_paternal/output.ktab input_files/paternal.ktab
19 && mv "\$(find ktabfiles_paternal -type f -name '*.ktab.1')" "input_files/.paternal.ktab.1" 19 && mv ktabfiles_paternal/.*.ktab* input_files/.paternal.ktab.1
20 && ln -s '$child_ktab_tar' child.tar 20 && ln -s '$child_ktab_tar' child.tar
21 && tar -xf child.tar 21 && tar -xf child.tar
22 && mv ktabfiles ktabfiles_child 22 && mv ktabfiles ktabfiles_child
23 && mv ktabfiles_child/output.ktab input_files/child.ktab 23 && mv ktabfiles_child/output.ktab input_files/child.ktab
24 && mv "\$(find ktabfiles_child -type f -name '*.ktab.1')" "input_files/.child.ktab.1" 24 && mv ktabfiles_child/.*.ktab* input_files/.child.ktab.1
25 && HAPmaker -v 25 && HAPmaker -v
26 -T\${GALAXY_SLOTS:-4} 26 -T\${GALAXY_SLOTS:-1}
27 input_files/maternal.ktab 27 input_files/maternal.ktab
28 input_files/paternal.ktab 28 input_files/paternal.ktab
29 input_files/child.ktab 29 input_files/child.ktab
30 && mv input_files/.*.hap* hapmaker_ktabs 30 && mv input_files/.*.hap* hapmaker_ktabs
31 && tar -czvf HapK_ktab_files.tar.gz hapmaker_ktabs 31 && tar -czvf HapK_ktab_files.tar.gz hapmaker_ktabs
34 <param name="maternal_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of maternal ktab file from FastK"/> 34 <param name="maternal_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of maternal ktab file from FastK"/>
35 <param name="paternal_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of paternal ktab file from FastK"/> 35 <param name="paternal_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of paternal ktab file from FastK"/>
36 <param name="child_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of child ktab file from FastK"/> 36 <param name="child_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of child ktab file from FastK"/>
37 </inputs> 37 </inputs>
38 <outputs> 38 <outputs>
39 <data name="paternal_out" format="fastk_ktab" from_work_dir="paternal.hap.ktab" label="${tool.name} on ${on_string}: paternal hap-mers"/> 39 <data name="paternal_out" format="fastk_ktab" from_work_dir="input_files/paternal.hap.ktab" label="${tool.name} on ${on_string}: paternal hap-mers"/>
40 <data name="maternal_out" format="fastk_ktab" from_work_dir="maternal.hap.ktab" label="${tool.name} on ${on_string}: maternal hap-mers"/> 40 <data name="maternal_out" format="fastk_ktab" from_work_dir="input_files/maternal.hap.ktab" label="${tool.name} on ${on_string}: maternal hap-mers"/>
41 <data name="intermediate_ktab" format="fastk_ktab_tar" from_work_dir="HapK_ktab_files.tar.gz" label="${tool.name} on ${on_string}: HapMaker Intermediate Ktab files"/> 41 <data name="intermediate_ktab" format="fastk_ktab_tar" from_work_dir="HapK_ktab_files.tar.gz" label="${tool.name} on ${on_string}: HapMaker Intermediate Ktab files"/>
42 </outputs> 42 </outputs>
43 <tests> 43 <tests>
44 <test expect_num_outputs="3"> 44 <test expect_num_outputs="3">
45 <param name="maternal_ktab_tar" ftype="fastk_ktab_tar" value="maternal.tar"/> 45 <param name="maternal_ktab_tar" ftype="fastk_ktab_tar" location="https://zenodo.org/records/14965629/files/maternal.fastk_ktab_tar"/>
46 <param name="paternal_ktab_tar" ftype="fastk_ktab_tar" value="paternal.tar"/> 46 <param name="paternal_ktab_tar" ftype="fastk_ktab_tar" location="https://zenodo.org/records/14965629/files/paternal.fastk_ktab_tar"/>
47 <param name="child_ktab_tar" ftype="fastk_ktab_tar" value="child.tar"/> 47 <param name="child_ktab_tar" ftype="fastk_ktab_tar" location="https://zenodo.org/records/14965629/files/child.fastk_ktab_tar"/>
48 <output name="paternal_out" value="paternal.hap.ktab"/> 48 <output name="paternal_out" ftype="fastk_ktab">
49 <output name="maternal_out" value="maternal.hap.ktab"/> 49 <assert_contents>
50 <has_size value="524304" delta="2000"/>
51 </assert_contents>
52 </output>
53 <output name="maternal_out" ftype="fastk_ktab">
54 <assert_contents>
55 <has_size value="524304" delta="2000"/>
56 </assert_contents>
57 </output>
50 <output name="intermediate_ktab" ftype="fastk_ktab_tar"> 58 <output name="intermediate_ktab" ftype="fastk_ktab_tar">
51 <assert_contents> 59 <assert_contents>
52 <has_archive_member path="hapmaker_ktabs/.maternal.hap.ktab.1"/> 60 <has_archive_member path="hapmaker_ktabs/.maternal.hap.ktab.1"/>
53 <has_archive_member path="hapmaker_ktabs/.paternal.hap.ktab.1"/> 61 <has_archive_member path="hapmaker_ktabs/.paternal.hap.ktab.1"/>
54 </assert_contents> 62 </assert_contents>
55 </output> 63 </output>
56 </test> 64 </test>
57 </tests> 65 </tests>
58 <help><![CDATA[ 66 <help><![CDATA[
59 HAPmaker generates hap-mer tables for parental datasets for merquryfk pipeline. Before running HAPplot or MerquryFK in trio mode, it is necessary to generate a table of hap-mers 67 HAPmaker generates hap-mer tables for parental datasets for merquryfk pipeline. Before running HAPplot or MerquryFK in trio mode, it is necessary to generate a table of hap-mers