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comparison hapmaker.xml @ 0:5eb60882a2a8 draft

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planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
author iuc
date Wed, 19 Feb 2025 11:21:31 +0000
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1 <tool id="merquryfk_hapmaker" name="MerquryFK HAPmaker" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
2 <description>Generates hap-mer tables from FastK k-mer data of maternal, paternal, and child sequences</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p input_files
9 && mkdir -p hapmaker_ktabs
10 && ln -s '$maternal_ktab_tar' maternal.tar
11 && tar -xf maternal.tar
12 && mv ktabfiles ktabfiles_maternal
13 && mv ktabfiles_maternal/output.ktab input_files/maternal.ktab
14 && mv "\$(find ktabfiles_maternal -type f -name '*.ktab.1')" "input_files/.maternal.ktab.1"
15 && ln -s '$paternal_ktab_tar' paternal.tar
16 && tar -xf paternal.tar
17 && mv ktabfiles ktabfiles_paternal
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"
20 && ln -s '$child_ktab_tar' child.tar
21 && tar -xf child.tar
22 && mv ktabfiles ktabfiles_child
23 && mv ktabfiles_child/output.ktab input_files/child.ktab
24 && mv "\$(find ktabfiles_child -type f -name '*.ktab.1')" "input_files/.child.ktab.1"
25 && HAPmaker -v
26 -T\${GALAXY_SLOTS:-4}
27 input_files/maternal.ktab
28 input_files/paternal.ktab
29 input_files/child.ktab
30 && mv input_files/.*.hap* hapmaker_ktabs
31 && tar -czvf HapK_ktab_files.tar.gz hapmaker_ktabs
32 ]]></command>
33 <inputs>
34 <param name="maternal_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of maternal ktab file from FastK"/>
35 <param name="paternal_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of paternal ktab file from FastK"/>
36 <param name="child_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of child ktab file from FastK"/>
37 </inputs>
38 <outputs>
39 <data name="paternal_out" format="fastk_ktab" from_work_dir="paternal.hap.ktab" label="${tool.name} on ${on_string}: paternal hap-mers"/>
40 <data name="maternal_out" format="fastk_ktab" from_work_dir="maternal.hap.ktab" label="${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"/>
42 </outputs>
43 <tests>
44 <test expect_num_outputs="3">
45 <param name="maternal_ktab_tar" ftype="fastk_ktab_tar" value="maternal.tar"/>
46 <param name="paternal_ktab_tar" ftype="fastk_ktab_tar" value="paternal.tar"/>
47 <param name="child_ktab_tar" ftype="fastk_ktab_tar" value="child.tar"/>
48 <output name="paternal_out" value="paternal.hap.ktab"/>
49 <output name="maternal_out" value="maternal.hap.ktab"/>
50 <output name="intermediate_ktab" ftype="fastk_ktab_tar">
51 <assert_contents>
52 <has_archive_member path="hapmaker_ktabs/.maternal.hap.ktab.1"/>
53 <has_archive_member path="hapmaker_ktabs/.paternal.hap.ktab.1"/>
54 </assert_contents>
55 </output>
56 </test>
57 </tests>
58 <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
60 for both the mother and father, using FastK k-mer tables from the maternal, paternal, and child sequence data sets.
61 The output of this process produces two k-mer tables: <mat>.hap.ktab for the maternal hap-mers and <pat>.hap.ktab for the paternal hap-mers.
62 ]]></help>
63 <expand macro="citation"/>
64 </tool>