<tool id="copyrighter" name="CopyRighter" version="0.45">

  <description>trait bias corrector for microbial profiles</description>

  <requirements>
    <requirement type="binary">copyrighter</requirement>
  </requirements>

  <version_string>copyrighter --version</version_string>

  <command>
    copyrighter
      -i $input
      -d $database.value
      #if str($lookup):
        -l $lookup
      #end if
      #if str($total) != "None":
        -t $total
      #end if
      #if str($verbose):
        -v
      #end if
  </command>

  <inputs>
    <param name="input" type="data" format="txt" label="Input community file" help="Text file obtained from 16S rRNA microarray, 16S rRNA amplicon sequencing or metagenomic sequencing, in biom, QIIME, GAAS, Unifrac, or generic (tabular site-by-species) format. The file must contain read counts (not percentages) and taxa must have UNALTERED taxonomic assignments." />
    <conditional name="database">
      <param name="specify" type="select" label="Trait database" help="Tab-delimited file of traits: 16S copy number, genome length, ...">
        <option value="builtin">Built-in file</option>
        <option value="uploaded">Uploaded file</option>
      </param>
      <when value="builtin">
        <param name="value" type="select" label="Built-in file">
          <options from_data_table="trait_db" />
          <validator type="no_options" message="No built-in trait database is available"/>
        </param>
      </when>
      <when value="uploaded">
        <param name="value" type="data" format="tabular" label="Uploaded file" />
      </when>
    </conditional>
    <param name="lookup" type="select" display="radio" value="desc" label="Lookup method" help="What to match when looking up the trait value of a taxon.">
      <option value="desc">OTU name</option>
      <option value="id">OTU ID (if recorded in your input community file)</option>
    </param>
    <param name="total" type="data" format="tabular" optional="true" label="Total abundance file" help="Tab-delimited file containing the total microbial abundance of each community, e.g. 16S rRNA quantitative PCR numbers to be corrected by the average 16S rRNA copy number." />
    <param name="verbose" type="boolean" checked="no" truevalue="1" falsevalue="0" format="txt" label="Verbose" help="Display trait value assignments." />
  </inputs>

  <outputs>
    <data format="txt" name="relative" from_work_dir="out_copyrighted.txt" label="${tool.name} from ${on_string} (relative)"/>
    <data format="tabular" name="absolute" from_work_dir="out_copyrighted_total.tsv" label="${tool.name} from ${on_string} (absolute)">
      <filter>str(total) != "None"</filter>
    </data>
    <data format="txt" name="combined" from_work_dir="out_copyrighted_combined.txt" label="${tool.name} from ${on_string} (combined)">
      <filter>str(total) != "None"</filter>
    </data>
  </outputs>

  <stdio>
    <exit_code range="1:"  level="fatal" />
    <regex match="error|exception|invalid" source="stderr" level="fatal" />
  </stdio>

  <tests>
    <test>
      <param name="input" value="test_data/in.qiime" />
      <param name="specify" value="uploaded"/>
      <param name="value" value="test_data/in_db.tsv"/>
      <output name="relative" file="test_data/out.qiime"/>
    </test>
    <test>
      <param name="input" value="test_data/in.biom"/>
      <param name="specify"  value="uploaded"/>
      <param name="value" value="test_data/in_db.tsv"/>
      <output name="relative" file="test_data/out.biom" lines_diff="2"/>
    </test>
    <test>
      <param name="input" value="test_data/in.qiime"/>
      <param name="specify"  value="uploaded"/>
      <param name="value" value="test_data/in_db.tsv"/>
      <param name="verbose" value="yes"/>
      <output name="relative" file="test_data/out.qiime"/>
    </test>
    <test>
      <param name="input" value="test_data/in.biom"/>
      <param name="specify"  value="uploaded"/>
      <param name="value" value="test_data/in_db.tsv"/>
      <param name="lookup" value="id"/>
      <output name="relative" file="test_data/out2.biom" lines_diff="2"/>
    </test>
    <test>
      <param name="input" value="test_data/in.qiime"/>
      <param name="specify"  value="uploaded"/>
      <param name="value" value="test_data/in_db.tsv"/>
      <param name="total" value="test_data/in_total.tsv"/>
      <output name="relative" file="test_data/out.qiime"/>
      <output name="absolute" file="test_data/out_total.tsv"/>
      <output name="combined" file="test_data/out_combined.qiime"/>
    </test>
    <!--<test>
      <param name="input" value="test_data/in.biom"/>
      <param name="specify"  value="builtin"/>
      <param name="value" value="test_data/in_db.tsv"/>
      <output name="relative" file="test_data/out.biom" lines_diff="2"/>
    </test>-->
  </tests>

  <help>
**What CopyRighter does**

The genome of Bacteria and Archaea often contains several copies of the
16S rRNA gene. This can lead to significant biases when estimating the
composition of microbial communities using 16S rRNA amplicons or
microarrays or their total abundance using 16S rRNA quantitative PCR,
since species with a large number of copies will contribute
disproportionally more 16S amplicons than species with a unique copy.
Fortunately, it is possible to infer the copy number of unsequenced
microbial species, based on that of close relatives that have been fully
sequenced. Using this information, CopyRigher corrects microbial
relative abundance by applying a weight proportional to the inverse of
the estimated copy number to each species.

In metagenomic surveys, a similar problem arises due to genome length
variations between species, and can be corrected by CopyRighter as well.

In all cases, a community file is used as input and a corrected community
file with trait-corrected (16S rRNA gene copy number or genome length)
relative abundances is generated. Total abundance can optionally be
provided, corrected and combined with relative abundance estimates to
get the absolute abundance of each species. Also the average trait value
in each community is reported on standard output.
  </help>

</tool>