Mercurial > repos > iuc > humann_strain_profiler

annotate humann_strain_profiler.xml @ 0:0ff86e44895c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
author iuc
date Wed, 12 May 2021 09:03:21 +0000
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0ff86e44895c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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1 <tool id="humann_strain_profiler" name="Make strain profiles" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0ff86e44895c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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2 <description></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="edam_ontology"/>
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7 <expand macro="requirements"/>
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8 <expand macro="version"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 humann_strain_profiler
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11 --input '$input'
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12 --critical_mean $critical_mean
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13 --critical_count $critical_count
0ff86e44895c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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14 --pinterval $pinterval_1 $pinterval_2
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15 --critical_samples $critical_samples
0ff86e44895c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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16 #if str($limit) != ''
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17 --limit '$limit'
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18 #end if
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19 ]]></command>
0ff86e44895c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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20 <inputs>
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21 <param argument="--input" type="data" format="tsv,tabular,biom1" label="Merged gene families output for two or more samples"/>
0ff86e44895c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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22 <param argument="--critical_mean" type="float" value="10.0" label="Default mean non-zero gene abundance for inclusion"/>
0ff86e44895c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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23 <param argument="--critical_count" type="integer" value="500" label="Default non-zero number of genes for inclusion"/>
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24 <param name="pinterval_1" type="float" value="1e-10" label="Low prevalence threshold" help="Only genes with prevalence higher than the threshold are allowed"/>
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25 <param name="pinterval_2" type="float" value="1" label="High prevalence threshold" help="Only genes with prevalence lower than the threshold are allowed"/>
0ff86e44895c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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26 <param argument="--critical_samples" type="integer" value="2" label="Threshold number of samples having strain"/>
0ff86e44895c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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27 <param argument="--limit" type="text" value="" optional="true" label="Limit output to species matching a particular pattern?" help="e.g. 'Streptococcus'"/>
0ff86e44895c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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28 </inputs>
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29 <outputs>
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30 <collection name="output" type="list">
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31 <discover_datasets pattern="(?P&lt;designation&gt;.+)-strain_profile.tsv" format="tabular" directory="."/>
0ff86e44895c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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32 </collection>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input" value="strain_profiler-input.txt"/>
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37 <param name="critical_mean" value="1"/>
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38 <param name="critical_count" value="2"/>
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39 <param name="pinterval_1" value="1e-10"/>
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40 <param name="pinterval_2" value="1"/>
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41 <param name="critical_samples" value="2"/>
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42 <output_collection name="output" type="list">
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43 <element name="s1" ftype="tabular">
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44 <assert_contents>
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45 <has_text text="A|g1.s1"/>
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46 <has_text text="10.0"/>
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47 <has_n_columns n="4"/>
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48 </assert_contents>
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49 </element>
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50 <element name="s2" ftype="tabular">
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51 <assert_contents>
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52 <has_text text="A|g1.s2"/>
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53 <has_text text="10.0"/>
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54 <has_n_columns n="4"/>
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55 </assert_contents>
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56 </element>
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57 </output_collection>
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 @HELP_HEADER@
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62
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63 This tool makes strain profiles, based on the principle of detecting variable
0ff86e44895c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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64 presence and absence of gene families within a species
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65 that is otherwise well-covered in multiple samples.
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66 ]]></help>
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67 <expand macro="citations"/>
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68 </tool>