Mercurial > repos > iuc > checkm_lineage_set

annotate lineage_set.xml @ 2:3693acdbf0d6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 3ae2bd72f789518e95ef65b97e0e5ac90165e113
author iuc
date Mon, 02 Sep 2024 13:50:42 +0000
parents b39999cdbf21
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b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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1 <tool id="checkm_lineage_set" name="CheckM lineage_set" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>
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3 Infer lineage-specific marker sets for each bin
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="biotools"/>
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9 <expand macro="requirements"/>
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10 <expand macro="version"/>
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11 <command detect_errors="exit_code"><![CDATA[
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12 @HMM_MARKER_STATS_INPUTS@
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13 mkdir 'inputs/storage/tree' &&
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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14 ln -s '$concatenated_tre' 'inputs/storage/tree/concatenated.tre' &&
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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15
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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16 checkm lineage_set
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17 'inputs'
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18 '$marker'
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19 --unique $unique
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20 --multi $multi
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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21 $force_domain
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22 $no_refinement
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23 ]]></command>
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24 <inputs>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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25 <expand macro="hmm_marker_stats_inputs"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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26 <param name="concatenated_tre" type="data" format="phyloxml" label="Concatenated tree" help="Output of the CheckM tree tool"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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27 <expand macro="lineage_set_params" />
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28 </inputs>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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29 <outputs>
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30 <expand macro="marker_output" />
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31 </outputs>
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32 <tests>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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33 <test expect_num_outputs="1">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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34 <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
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35 <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
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36 <param name="hmmer_tree">
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37 <collection type="list">
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38 <element name="637000110" ftype="txt" value="hmmer.tree.txt"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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39 </collection>
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40 </param>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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41 <param name="concatenated_tre" ftype="phyloxml" value="concatenated.tre"/>
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42 <param name="unique" value="10"/>
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43 <param name="multi" value="10"/>
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44 <param name="force_domain" value="false"/>
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45 <param name="no_refinement" value="false"/>
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46 <output name="marker" ftype="tabular">
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47 <assert_contents>
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48 <has_text text="637000110"/>
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49 <has_text text="Lineage Marker File"/>
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50 <has_text text="PF00203"/>
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51 </assert_contents>
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52 </output>
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53 </test>
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54 </tests>
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55 <help><![CDATA[
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56 @HELP_HEADER@
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57
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58 This command places bins in the genome tree.
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59 ]]></help>
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60 <expand macro="citations"/>
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61 </tool>