Mercurial > repos > iuc > profile2cami
annotate taxonkit_profile2cami.xml @ 4:d38b9fdf04e0 draft default tip
planemo upload for repository https://github.com/shenwei356/taxonkit commit 491bc028e8546bee626ab6f6168a706ab2f5324a
author | iuc |
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date | Mon, 04 Nov 2024 22:07:39 +0000 (7 weeks ago) |
parents | 0fd79958fac6 |
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rev | line source |
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0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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1 <tool id="profile2cami" name="Profile2CAMI" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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2 <description>Convert metagenomic profile table to CAMI format</description> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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3 <macros> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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4 <import>macros.xml</import> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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5 </macros> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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6 <expand macro="biotools"/> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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7 <expand macro="requirements" /> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
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8 <command detect_errors="exit_code"> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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9 <![CDATA[ |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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10 taxonkit profile2cami |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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11 --data-dir '${taxonomy.fields.path}' |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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12 --abundance-field '${abundance_field}' |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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13 --taxid-field '${taxid_field}' |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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14 |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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15 $percentage |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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16 $recompute_abd |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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17 $keep_zero |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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parents:
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18 $no_sum_up |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
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19 |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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20 #if $sample_id: |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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21 -s '${sample_id}' |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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22 #end if |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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23 #if $taxonomy_id: |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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24 -t '${taxonomy_id}' |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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25 #end if |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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26 #if $ranks: |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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27 --show-rank '${ranks}' |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
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28 #end if |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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parents:
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29 ${input_file} |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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30 > '${cami_output}' |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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31 ]]> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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parents:
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32 </command> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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33 <inputs> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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parents:
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34 <param name="input_file" type="data" format="txt" label="Input Profile File" help="A tab-delimited profile file with TaxId and abundance columns." /> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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35 <param argument="--taxonomy" type="select" label="NCBI taxonomy" help="This NCBI database is used to map human-readable taxon names to TaxId's."> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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36 <options from_data_table="ncbi_taxonomy"> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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37 <validator message="No NCBI database is available" type="no_options"/> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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parents:
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38 </options> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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39 </param> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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40 <param name="abundance_field" type="integer" value="2" label="Abundance Field Index" help="Field index of abundance in the input data." /> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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parents:
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41 <param name="taxid_field" type="integer" value="1" label="TaxId Field Index" help="Field index of TaxId in the input data." /> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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parents:
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42 <param name="percentage" type="boolean" value="false" label="Abundance in Percentage" help="Check if the abundance values are in percentage." truevalue="-p" falsevalue=""/> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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43 <param name="recompute_abd" type="boolean" value="false" label="Recompute Abundance" help="Check to recompute abundance if some TaxIds are deleted in the current taxonomy version." truevalue="-R" falsevalue=""/> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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44 <param name="keep_zero" type="boolean" value="false" label="Keep Zero Abundances" help="Check to keep taxons with abundance of zero." truevalue="-0" falsevalue=""/> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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45 <param name="no_sum_up" type="boolean" value="false" label="Do Not Sum Up Abundance" help="Do not sum up abundance from child to parent TaxIds." truevalue="-S" falsevalue="" /> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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46 <param name="sample_id" type="text" value="" label="Sample ID" help="Optional sample ID to include in the result file." /> |
0fd79958fac6
planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
parents:
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47 <param name="taxonomy_id" type="text" value="" label="Taxonomy ID" help="Optional taxonomy ID to include in the result file." /> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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48 <param name ="ranks" argument="--show-rank" type="select" multiple="true" label="Show Ranks" help="Specify the ranks to show in the result file (default [superkingdom,phylum,class,order,family,genus,species,strain])."> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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49 <option value="superkingdom">Superkingdom</option> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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50 <option value="phylum">Phylum</option> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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51 <option value="class">Class</option> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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52 <option value="order">Order</option> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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53 <option value="family">Family</option> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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54 <option value="genus">Genus</option> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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55 <option value="species">Species</option> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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56 <option value="strain">Strain</option> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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57 </param> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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58 </inputs> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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59 <outputs> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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60 <data name="cami_output" format="tsv" label="${tool.name} on ${on_string}" /> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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61 </outputs> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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62 <tests> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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63 <!-- Test 1: Basic functionality with default parameters --> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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64 <test expect_num_outputs="1"> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
iuc
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65 <param name="input_file" value="abundance.tsv" ftype="tsv" /> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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66 <output name="cami_output" file="output1_basic_functionality.tsv" /> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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67 </test> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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68 |
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69 <!-- Test 2: Using percentage flag --> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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70 <test expect_num_outputs="1"> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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71 <param name="input_file" value="abundance.tsv" ftype="tsv" /> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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72 <param name="percentage" value="true" /> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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73 <output name="cami_output" file="output2_percentage_flag.tsv" /> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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74 </test> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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75 |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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76 <!-- Test 3: Recomputing abundance with deleted TaxIds --> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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77 <test expect_num_outputs="1"> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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78 <param name="input_file" value="abundance.tsv" ftype="tsv" /> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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79 <param name="recompute_abd" value="true" /> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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80 <output name="cami_output" file="output3_recompute_abd.tsv" /> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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81 </test> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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82 |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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83 <!-- Test 4: Profile2Cami with all parameters checked --> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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84 <test expect_num_outputs="1"> |
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planemo upload for repository https://github.com/shenwei356/taxonkit commit 695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82
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85 <param name="input_file" value="abundance.tsv" ftype="tsv" /> |
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86 <param name="percentage" value="true" /> |
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87 <param name="recompute_abd" value="true" /> |
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88 <param name="keep_zero" value="true" /> |
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89 <param name="no_sum_up" value="true" /> |
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90 <output name="cami_output" file="output4_all_param.tsv" /> |
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91 </test> |
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92 </tests> |
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93 <help> |
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94 <![CDATA[ |
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95 **What is Profile2CAMI** |
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96 |
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97 Profile2CAMI is a tool for converting metagenomic profile tables to CAMI format. |
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98 |
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99 **Inputs** |
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100 |
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101 - A tab-delimited profile file with TaxId and abundance columns. |
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102 |
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103 **Outputs** |
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104 |
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105 - A CAMI formatted file. |
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106 |
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107 For more information, please refer to the tool's documentation. |
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108 ]]> |
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109 </help> |
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110 <expand macro="citations" /> |
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111 </tool> |