Mercurial > repos > jdv > gottcha
annotate gottcha.xml @ 0:2569a83977f5 draft
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
author | jdv |
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date | Mon, 30 Jan 2017 19:07:21 -0500 |
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children | 87efdde6105f |
rev | line source |
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0
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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1 <tool id="gottcha" name="GOTTCHA" version="0.0.1"> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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2 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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3 <description>Read-based metagenome characterization</description> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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4 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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5 <!-- ***************************************************************** --> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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6 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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7 <requirements> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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8 <requirement type="package" version="1.0b-564cf3b">gottcha</requirement> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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9 </requirements> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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10 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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11 <!-- ***************************************************************** --> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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12 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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13 <version_command>gottcha.pl -h | perl -wnE'print "$1\n" for /VERSION: (\S+)/g'</version_command> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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14 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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changeset
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15 <!-- ***************************************************************** --> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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16 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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17 <command detect_errors="aggressive"> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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18 <![CDATA[ |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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19 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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20 gottcha.pl |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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21 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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22 --input '${fn_in}' |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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23 --database '${db.fields.path}' |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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24 --threads '\${GALAXY_SLOTS:-1}' |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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25 --outdir './' |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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26 --prefix results |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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27 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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28 ##--General Options------------------------------ |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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29 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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changeset
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30 --relAbu ${general.rel_abund} |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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31 --mode ${general.output_full} |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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32 ${general.filt_plasmid} |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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33 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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34 ##--Split-trim Options--------------------------- |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
diff
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35 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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36 --minQ ${split.min_qual} |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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37 --fixL ${split.fixed_len} |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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38 --ascii ${split.qual_offset} |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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39 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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40 ##--Filtering Options---------------------------- |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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41 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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42 --minCov ${filter.min_cov} |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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43 --minMLHL ${filter.min_mlhl} |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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44 --cCov ${filter.c_cov} |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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45 --minLen ${filter.min_len} |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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46 --minHits ${filter.min_hits} |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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47 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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48 ]]> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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49 </command> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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50 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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51 <!-- ***************************************************************** --> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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52 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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53 <inputs> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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54 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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55 <param name="fn_in" type="data" format="fastq" label="Input reads" help="--input" /> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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56 <param name="db" type="select" label="Select a reference database" help="--database"> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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57 <options from_data_table="gottcha_indices"> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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58 <filter type="sort_by" column="2"/> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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59 <validator type="no_options" message="No indexes are available for the selected input dataset"/> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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60 </options> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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61 </param> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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62 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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63 <section name="general" title="General Options" expanded="True"> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
parents:
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64 <param name="rel_abund" type="select" label="Abundance field" help="--relAbu"> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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65 <option value="LINEAR_DOC" selected="true">Linear DOC</option> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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66 <option value="LINEAR_LENGTH">Linear length</option> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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67 <option value="TOTAL_BP_MAPPED">Total bp mapped</option> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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68 <option value="HIT_COUNT">Hit count</option> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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69 </param> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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70 <param name="output_full" type="boolean" truevalue="full" falsevalue="summary" checked="no" label="Output full report" help="--mode full" /> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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71 <param name="filt_plasmid" type="boolean" truevalue="--noPlasmidHit" falsevalue="" checked="no" label="Filter plasmid hits" help="If true, ignore alignments to plasmids" /> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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72 </section> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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73 |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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74 <section name="split" title="Split-trim Options" expanded="False"> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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75 <param name="min_qual" size="4" type="integer" value="20" min="0" max="41" label="Minimum quality" help="Minimum quality for a read to be considered valid (0-41)" /> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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76 <param name="fixed_len" size="4" type="integer" value="30" min="1" label="Trim length" help="Fixed length to which each read will be trimmed" /> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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77 <param name="qual_offset" type="select" label="Quality offset" help="Base call quality offset for ASCII encoding"> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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78 <option value="33" selected="true">33</option> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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79 <option value="64">64</option> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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80 </param> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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81 </section> |
2569a83977f5
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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82 |
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83 <section name="filter" title="Filtering Options" expanded="False"> |
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84 <param name="min_cov" size="5" type="float" value="0.005" min="0" label="Minimum coverage" help="Minimum linear coverage to be considered valid in abundance calculation" /> |
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85 <param name="min_mlhl" size="4" type="integer" value="5" min="0" label="Minimum MLHL" help="Minimum mean-linear-hit-length to be considered valid in abundance calculations" /> |
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86 <param name="c_cov" size="5" type="float" value="0.006" min="0" label="Critical coverage for MLHL" help="Critical coverage below which Minimum MLHL will cause an organism to fail" /> |
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87 <param name="min_len" size="4" type="integer" value="100" min="0" label="Minimum length" help="Minimum unique length to be considered valid in abundance calculation" /> |
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88 <param name="min_hits" size="4" type="integer" value="10" min="0" label="Minimum hits" help="Minimum number of hits to be considered valid in abundance calculation" /> |
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89 </section> |
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90 |
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91 </inputs> |
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92 |
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93 <!-- ***************************************************************** --> |
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94 |
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95 <outputs> |
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96 |
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97 <data name="out_log" format="txt" label="GOTTCHA on ${on_string}: Log" from_work_dir="results.gottcha.log" /> |
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98 <data name="out_tsv" format="txt" label="GOTTCHA on ${on_string}: Summary" from_work_dir="results.gottcha.tsv" /> |
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99 <data name="out_full" format="txt" label="GOTTCHA on ${on_string}: Full Report" from_work_dir="results.gottcha_full.tsv"> |
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100 <filter>output_full</filter> |
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101 </data> |
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102 |
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103 </outputs> |
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104 |
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105 <!-- ***************************************************************** --> |
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106 |
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107 <tests> |
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108 <test> |
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109 <param name="db" value="test_db" /> |
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110 <param name="fn_in" ftype="fastq" value="test.fq" /> |
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111 <param name="output_full" value="no" /> |
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112 <param name="min_hits" value="1" /> |
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113 <output name="out_tsv" file="test_02.tsv" /> |
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114 <output name="out_log" file="test_02.log" compare="sim_size" delta="2000"/> |
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115 </test> |
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116 </tests> |
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117 |
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118 <!-- ***************************************************************** --> |
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119 |
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120 <help> |
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121 <![CDATA[ |
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122 |
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123 .. class:: infomark |
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124 |
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125 Description |
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126 -------------------- |
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127 |
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128 Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) is an |
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129 annotation-independent and signature-based metagenomic taxonomic profiling |
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130 tool that has significantly smaller FDR than other profiling tools. This Perl |
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131 script is a wrapper to run the GOTTCHA profiling tool with pre-computed |
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132 signature databases. The procedure includes 3 major steps: split-trimming the |
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133 input data, mapping reads to a GOTTCHA database using BWA, profiling/filtering |
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134 the result. |
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135 |
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136 Options |
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137 -------------------- |
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138 :: |
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139 |
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140 --relAbu|r <STRING> The field will be used to calculate relative |
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141 abundance. You can specify one of the following |
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142 fields: "LINEAR_LENGTH", "TOTAL_BP_MAPPED", |
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143 "HIT_COUNT", "LINEAR_DOC". |
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144 [default: LINEAR_DOC] |
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145 --mode|m <STRING> You can specify one of the output mode: |
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146 "summary" : this mode will report a summary of |
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147 profiling result to *.gottcha.tsv file. |
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148 "full" : other than a summary, this mode will |
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149 report unfiltered result to |
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150 *.gottcha_full.tsv with more detail. |
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151 "all" : other than two tables, this mode will |
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152 keep all output files that were |
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153 generated by each profiling step. |
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154 [default: summary] |
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155 --noPlasmidHit|n Ignore alignments that hit to plasmids |
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156 [default: null] |
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157 |
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158 *** OPTIONS FOR SPLIT-TRIMMING READS *** |
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159 |
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160 --minQ <INT> Minimum quality for a read to be considered valid |
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161 (0-41) [default: 20] |
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162 --fixL <INT> Fixed length to which each trimmed read will be cut |
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163 down to [default: 30] |
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164 --ascii <INT> ASCII encoding of quality score (33 or 64) [default: |
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165 33] |
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166 |
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167 *** OPTIONS FOR FILTERING PROFILING RESULT *** |
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168 |
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169 --minCov <FLOAT> Minimum linear coverage to be considered valid in |
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170 abundance calculation [default: 0.005] |
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171 --minMLHL <INT> Minimum Mean-Linear-Hit-Length to be considered valid |
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172 in abundance calculation [default: 5] |
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173 --cCov <FLOAT> Critical coverage below which --minMLHL will cause an |
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174 organism to fail [default: 0.006] |
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175 --minLen <INT> Minimum unique length to be considered valid in |
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176 abundance calculation [default: 100] |
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177 --minHits <INT> Minimum number of hits to be considered valid in |
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178 abundance calculation [10] |
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179 |
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180 Interpreting Results |
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181 -------------------- |
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182 |
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183 GOTTCHA reports profiling results in a neat summary table |
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184 by default. The tsv file will list the organism(s) at all taxonomic |
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185 levels from STRAIN to PHYLUM, their linear length, total bases mapped, |
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186 linear depth of coverage, and the normalized linear depth of coverage. The |
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187 linear depth of coverage (LINEAR_DOC) is used to calculate relative |
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188 abundance of each organism or taxonomic name in the sample. |
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189 |
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190 Summary table: |
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191 |
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192 ================= ============================== |
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193 Column Description |
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194 ================= ============================== |
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195 LEVEL taxonomic rank |
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196 NAME taxonomic name |
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197 REL_ABUNDANCE relative abundance (equivalent to NORM_COV by default) |
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198 LINEAR_LENGTH number of non-overlapping bases covering the signatures |
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199 TOTAL_BP_MAPPED sum total of all hit lengths recruited to signatures |
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200 HIT_COUNT number of hits recruited to signatures |
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201 HIT_COUNT_PLASMID number of hits recruited to signatures |
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202 READ_COUNT number of reads recruited to signatures |
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203 LINEAR_DOC linear depth-of-coverage (TOTAL_BP_MAPPED / LINEAR_LENGTH) |
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204 NORM_COV normalized linear depth-of-coverage (LINEAR_DOC / SUM(LINEAR_DOC in certain level)) |
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205 ================= ============================== |
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206 |
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207 Other than a summary table, "full" report mode will report a table with more |
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208 detail information from unfiltered results. The explanation of each column in |
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209 the full report is as follows: |
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210 |
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211 ================================== ========================== |
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212 Column Description |
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213 ================================== ========================== |
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214 RANKNAME (REPLICON) = replicon name (source + plasmid/chr)<br>(STRAIN) = strain name<br>(SPECIES) = species name<br>(GENUS) = genus name<br>... |
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215 NUM_SUBRANKS no. of distinct subranks for the current rank<br>(E.g. the no. of SPECIES under the current GENUS) |
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216 GPROJ_ENTRIES no. of genome projects (i.e. STRAINS) under this RANK NAME |
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217 LINEAR_LENGTH N/O_LENGTH<br>= non-overlapping length <br>= no. of non-overlapping bases covering the unique DB |
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218 UNIQUE_DB_LENGTH no. of unique bases for this organism |
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219 FULL_REFDB_LENGTH no. of bases in full reference |
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220 LINEAR_COV LINEAR_LENGTH / UNIQUE_DB_LENGTH |
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221 HIT_COUNT no. of hits recruited to genome |
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222 HIT_COUNT_PLASMID no. of hits recruited to plasmid |
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223 READ_COUNT no. of reads recruited to genome |
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224 FULL_HIT_COUNT no. of full-length read hits recruited to genome |
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225 TOTAL_BP_MAPPED sum total of all hit lengths recruited to genome<br>= hit1.length + hit2.length + ... hitX.length<br>[formerly FOLD_COV_UNIQUE_SAMPLE] |
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226 LINEAR_DOC linear depth-of-coverage<br>= fold coverage of sample's LINEAR_LENGTH <br>= TOTAL_BP_MAPPED / LINEAR_LENGTH<br>[formerly FOLD_COV_UNIQUE_REFDB] |
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227 UREF_DOC unique reference's depth-of-coverage<br>= fold coverage of reference's UNIQUE_DB_LENGTH<br>= TOTAL_BP_MAPPED / UNIQUE_DB_LENGTH |
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228 UREF_CMAX MAX COVERAGE OF REFDB POSSIBLE, GIVEN SAMPLE INPUT BASES<br>= Cmax = L0/l0 <br>= TOTAL_INPUT_BASES / UNIQUE_DB_LENGTH |
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229 FRAC_HITS_POSSIBLE HIT_COUNT / TOTAL_INPUT_READS |
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230 FRAC_BASES_POSSIBLE TOTAL_BP_MAPPED / TOTAL_INPUT_BASES |
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231 MEAN_HIT_LENGTH TOTAL_BP_MAPPED / HIT_COUNT |
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232 MEAN_LINEAR_HIT_LENGTH LINEAR_LENGTH / HIT_COUNT |
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233 best_SUBRANK name of the best subrank (determined by the highest LINEAR_COV) |
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234 best_NUM_SUBRANKS no. of subranks supporting current "SUBRANK"<br>{SS} = no. of GI entries supporting this strain<br>{S} = no. of strains supporting this species<br>{G} = no. of species supporting this genus<br>{F} = no. of genera supporting this family<br>{O} = no. of families supporting this order <br>{C} = no. of orders supporting this class<br>{P} = no. of classes supporting this phylum |
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235 best_GPROJ_ENTRIES no. of genome projects (i.e. STRAINS) under this best_SUBRANK<br>{SS} = no. of genome projects supporting this strain = 1<br>{S} = no. of genome projects supporting this species<br>{G} = no. of genome projects supporting this genus<br>{F} = no. of genome projects supporting this family<br>{O} = no. of genome projects supporting this order<br>{C} = no. of genome projects supporting this class<br>{P} = no. of genome projects supporting this phylum |
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236 best_LINEAR_LENGTH |
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237 best_UNIQUE_DB_LENGTH |
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238 best_FULL_REFDB_LENGTH |
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239 best_LINEAR_COV |
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240 best_HIT_COUNT |
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241 best_FULL_HIT_COUNT |
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242 best_TOTAL_BP_MAPPED |
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243 best_LINEAR_DOC (a.k.a. Abundance) |
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244 best_UREF_DOC |
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245 best_UREF_CMAX |
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246 best_FRAC_HITS_POSSIBLE |
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247 best_FRAC_BASES_POSSIBLE |
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248 best_MEAN_HIT_LENGTH |
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249 best_MEAN_LINEAR_HIT_LENGTH |
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250 CONTIG_COUNT no. of contiguous fragments<br> (after mapping & generating non-overlapping fragments) |
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251 CONTIG_MEAN_LEN mean length of contigs (bp) |
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252 CONTIG_STDEV_LEN standard deviation of contig lengths (bp) |
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253 CONTIG_MINLEN length of smallest contig |
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254 CONTIG_MAXLEN length of largest contig |
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255 CONTIG_HISTOGRAM(LEN:FREQ) contig Length Histogram<br> (in the format contigLength:frequency) |
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256 ================================== ========================== |
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257 |
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258 ]]> |
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259 </help> |
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260 |
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261 <!-- ***************************************************************** --> |
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262 |
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263 <citations> |
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264 <citation type="doi">10.1093/nar/gkv180</citation> |
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265 </citations> |
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266 |
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267 </tool> |