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annotate kraken_biom.xml @ 2:b582a159bb10 draft default tip

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planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 79f3b3dd54ec6d401563f965ba93b7fca4cadda6
author iuc
date Mon, 11 Mar 2024 16:01:58 +0000
parents 65eb9962d272
children
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3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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1 <tool id="kraken_biom" name="Kraken-biom" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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2 <description>Create BIOM-format tables from kraken output</description>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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3 <macros>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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4 <import>macros.xml</import>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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5 </macros>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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6 <expand macro="requirements"/>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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7 <version_command>kraken-biom --version</version_command>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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8 <command detect_errors="exit_code"><![CDATA[
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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9 #for $i, $s in enumerate($kraken_reports)
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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10 #if $s
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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11 ln -s '$s' './$i-kraken_report.tabular' &&
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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12 #end if
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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13 #end for
1
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14 #if $metadata
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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15 ln -s '$metadata' './metadata.tsv' &&
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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16 #end if
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3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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17 kraken-biom
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18 #for $i, $s in enumerate($kraken_reports)
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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19 #if $s
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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20 '$i-kraken_report.tabular'
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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21 #end if
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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22 #end for
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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23 #if $max
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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24 --max $max
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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25 #end if
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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26 #if $min
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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27 --min $min
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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28 #end if
1
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29 #if $metadata
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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30 --metadata 'metadata.tsv'
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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31 #end if
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32 #if $otu_fp
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33 --otu_fp 'OTU_FP'
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34 #end if
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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35 #if $fmt
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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36 --fmt $fmt
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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37 #end if
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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38 ]]></command>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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39 <inputs>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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40 <param name="kraken_reports" type="data" multiple="true" format="tabular" label="Input files to Kraken-biom: Kraken report output file(s)"/>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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41 <param argument="--max" type="select" optional="true" label="Max" help="Assigned reads will be recorded only if they are at or below max rank. Default: O">
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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42 <option value="O" selected="true">O</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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43 <option value="D">D</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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44 <option value="P">P</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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45 <option value="C">C</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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46 <option value="F">F</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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47 <option value="G">G</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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48 <option value="S">S</option>
1
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49 <option value="SS">SS</option>
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3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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50 </param>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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51 <param argument="--min" type="select" optional="true" label="Min" help="Reads assigned at and below min rank will be recorded as being assigned to the min rank level. Default: S">
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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52 <option value="O">O</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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53 <option value="D">D</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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54 <option value="P">P</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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55 <option value="C">C</option>
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56 <option value="F">F</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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57 <option value="G">G</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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58 <option value="S" selected="true">S</option>
1
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59 <option value="SS">SS</option>
0
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60 </param>
1
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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61 <param argument="--metadata" type="data" format="tabular" optional="true" label="Sample metadata file" help="This should be in TSV or CSV (Tabular) format. The first column should be the Sample ID (e.g. 0-kraken_report, 1-kraken_report, etc.). This is the same name as the input files. If no metadata is given, basic metadata is added to support importing the BIOM table into sites like phinch (http://phinch.org/index.html). Example for metadata files: http://qiime.org/documentation/ file_formats.html#mapping-file-overview"/>
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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62 <param name="otu_fp" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Do you want to create an OTU IDs file" help="Create a file containing just the (NCBI) OTU IDs for use with a service such as phyloT (http://phylot.biobyte.de/) to generate a phylogenetic tree for use in downstream analysis such as UniFrac, iTol (itol.embl.de), or PhyloToAST (phylotoast.org)"/>
0
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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63 <param argument="--fmt" type="select" optional="true" label="Output Format" help="Set the output format of the BIOM table. Default is HDF5">
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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64 <option value="tsv">TSV</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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65 <option value="json">JSON</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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66 <option value="hdf5" selected="true">Biom2 (HDF5)</option>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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67 </param>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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68 </inputs>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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69 <outputs>
1
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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70 <data name="biomOutput" format="tabular" from_work_dir="./table.biom" label="Kraken-biom output file">
0
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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71 <change_format>
1
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72 <when input="fmt" value="json" format="biom1" />
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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73 </change_format>
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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74 <change_format>
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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75 <when input="fmt" value="hdf5" format="biom2" />
0
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76 </change_format>
1
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77 </data>
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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78 <data name="otuOutput" format="mothur.map" from_work_dir="./OTU_FP" label="OTU File">
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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79 <filter>otu_fp is True</filter>
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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80 </data>
0
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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81 </outputs>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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82 <tests>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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83 <test expect_num_outputs="1">
1
65eb9962d272 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit 345448a555041e515c3fca937cc123b5de794ca6
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84 <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/>
0
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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85 <param name="fmt" value="hdf5"/>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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86 <output name="biomOutput" ftype="biom2">
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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87 <assert_contents>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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88 <has_text text="creation-date"/>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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89 </assert_contents>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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90 </output>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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91 </test>
3ff4712dc111 planemo upload for repository https://github.com/smdabdoub/kraken-biom commit a7d3ae6f4ff1a49b1b329532379f5ccfafd573fa
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92 <test expect_num_outputs="1">
1
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93 <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/>
0
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94 <param name="fmt" value="tsv"/>
1
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95 <output name="biomOutput" ftype="tabular">
0
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96 <assert_contents>
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97 <has_n_lines n="8246"/>
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98 <has_text text="Constructed from biom file"/>
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99 </assert_contents>
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100 </output>
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101 </test>
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102 <test expect_num_outputs="1">
1
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103 <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/>
0
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104 <param name="fmt" value="json"/>
1
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105 <output name="biomOutput" ftype="biom1">
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106 <assert_contents>
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107 <has_text text="Biological Observation"/>
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108 </assert_contents>
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109 </output>
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110 </test>
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111 <test expect_num_outputs="2">
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112 <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/>
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113 <param name="otu_fp" value="true"/>
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114 <param name="fmt" value="json"/>
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115 <output name="biomOutput" ftype="biom1">
0
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116 <assert_contents>
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117 <has_text text="Biological Observation"/>
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118 </assert_contents>
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119 </output>
1
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120 <output name="otuOutput" ftype="mothur.map">
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121 <assert_contents>
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122 <has_n_lines n="8244"/>
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123 </assert_contents>
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124 </output>
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125 </test>
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126 <test expect_num_outputs="2">
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127 <param name="kraken_reports" value="MG_AIR20200707.tabular,MG_AIR20200708.tabular,MG_AIR20200709.tabular"/>
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128 <param name="metadata" value="SamplesMetaDataTabular.csv"/>
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129 <param name="otu_fp" value="true"/>
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130 <param name="fmt" value="json"/>
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131 <output name="biomOutput" ftype="biom1">
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132 <assert_contents>
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133 <has_text text="Biological Observation"/>
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134 </assert_contents>
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135 </output>
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136 <output name="otuOutput" ftype="mothur.map">
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137 <assert_contents>
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138 <has_n_lines n="8244"/>
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139 </assert_contents>
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140 </output>
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141 </test>
0
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142 </tests>
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143 <help><![CDATA[
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144 Kraken-biom
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145 ===========
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146 Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/).
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147
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148 Input
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149 =====
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150 The program takes as input, one or more files output from the kraken-report tool. Each file is parsed and the counts for each OTU (operational taxonomic unit) are recorded, along with database ID (e.g. NCBI), and lineage. The extracted data are then stored in a BIOM table where each count is linked to the Sample and OTU it belongs to. Sample IDs are extracted from the input filenames (everything up to the '.').
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151
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152 OTUs are defined by the --max and --min arguments. By default these are set to Order and Species respectively. This means that counts assigned directly to an Order, Family, or Genus are recorded under the associated OTU ID, and counts assigned at or below the Species level are assigned to the OTU ID for the species. Setting a minimum rank below Species is not yet available.
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153
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154 Output
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155 ======
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156 The BIOM format currently has two major versions. Version 1.0 uses the JSON (JavaScript Object Notation) format as a base. Version 2.x uses the HDF5 (Hierarchical Data Format v5) as a base. The output format can be specified with the --fmt option. Note that a tab-separated (tsv) output format is also available. The resulting file will not contain most of the metadata, but can be opened by spreadsheet programs.
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157
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158 Version 2 of the BIOM format is used by default for output, but requires the Python library 'h5py'. If the library is not installed, kraken-biom will automatically switch to using version 1.0. Note that the output can optionally be compressed with gzip (--gzip) for version 1.0 and TSV files. Version 2 files are automatically compressed.
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159 ]]></help>
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160 <citations>
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161 <citation type="bibtex">
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162 @misc{githubseqtk,
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163 author = {Dabdoub, SM},
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164 year = {2016},
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165 title = {kraken-biom},
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166 publisher = {GitHub},
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167 journal = {GitHub repository},
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168 url = {https://github.com/smdabdoub/kraken-biom},
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169 }</citation>
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170 </citations>
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171 </tool>