Mercurial > repos > iuc > merquryfk_hapmaker

annotate 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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5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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1 <tool id="merquryfk_hapmaker" name="MerquryFK HAPmaker" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
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2 <description>Generates hap-mer tables from FastK k-mer data of maternal, paternal, and child sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 mkdir -p input_files
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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9 && mkdir -p hapmaker_ktabs
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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10 && ln -s '$maternal_ktab_tar' maternal.tar
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11 && tar -xf maternal.tar
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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12 && mv ktabfiles ktabfiles_maternal
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13 && mv ktabfiles_maternal/output.ktab input_files/maternal.ktab
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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14 && mv "\$(find ktabfiles_maternal -type f -name '*.ktab.1')" "input_files/.maternal.ktab.1"
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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15 && ln -s '$paternal_ktab_tar' paternal.tar
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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16 && tar -xf paternal.tar
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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17 && mv ktabfiles ktabfiles_paternal
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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18 && mv ktabfiles_paternal/output.ktab input_files/paternal.ktab
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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19 && mv "\$(find ktabfiles_paternal -type f -name '*.ktab.1')" "input_files/.paternal.ktab.1"
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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20 && ln -s '$child_ktab_tar' child.tar
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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21 && tar -xf child.tar
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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22 && mv ktabfiles ktabfiles_child
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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23 && mv ktabfiles_child/output.ktab input_files/child.ktab
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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24 && mv "\$(find ktabfiles_child -type f -name '*.ktab.1')" "input_files/.child.ktab.1"
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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25 && HAPmaker -v
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26 -T\${GALAXY_SLOTS:-4}
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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27 input_files/maternal.ktab
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28 input_files/paternal.ktab
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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29 input_files/child.ktab
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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30 && mv input_files/.*.hap* hapmaker_ktabs
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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31 && tar -czvf HapK_ktab_files.tar.gz hapmaker_ktabs
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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32 ]]></command>
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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33 <inputs>
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34 <param name="maternal_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of maternal ktab file from FastK"/>
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35 <param name="paternal_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of paternal ktab file from FastK"/>
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36 <param name="child_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of child ktab file from FastK"/>
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37 </inputs>
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38 <outputs>
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39 <data name="paternal_out" format="fastk_ktab" from_work_dir="paternal.hap.ktab" label="${tool.name} on ${on_string}: paternal hap-mers"/>
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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40 <data name="maternal_out" format="fastk_ktab" from_work_dir="maternal.hap.ktab" label="${tool.name} on ${on_string}: maternal hap-mers"/>
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41 <data name="intermediate_ktab" format="fastk_ktab_tar" from_work_dir="HapK_ktab_files.tar.gz" label="${tool.name} on ${on_string}: HapMaker Intermediate Ktab files"/>
5eb60882a2a8 planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit 5c9fd72ef5aa8b8694cdba75d1e54fbe4cda5d9d
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42 </outputs>
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43 <tests>
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44 <test expect_num_outputs="3">
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45 <param name="maternal_ktab_tar" ftype="fastk_ktab_tar" value="maternal.tar"/>
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46 <param name="paternal_ktab_tar" ftype="fastk_ktab_tar" value="paternal.tar"/>
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47 <param name="child_ktab_tar" ftype="fastk_ktab_tar" value="child.tar"/>
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48 <output name="paternal_out" value="paternal.hap.ktab"/>
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49 <output name="maternal_out" value="maternal.hap.ktab"/>
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50 <output name="intermediate_ktab" ftype="fastk_ktab_tar">
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51 <assert_contents>
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52 <has_archive_member path="hapmaker_ktabs/.maternal.hap.ktab.1"/>
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53 <has_archive_member path="hapmaker_ktabs/.paternal.hap.ktab.1"/>
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54 </assert_contents>
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55 </output>
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56 </test>
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57 </tests>
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58 <help><![CDATA[
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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
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60 for both the mother and father, using FastK k-mer tables from the maternal, paternal, and child sequence data sets.
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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.
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62 ]]></help>
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63 <expand macro="citation"/>
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64 </tool>