<tool id="glytools_fingerprinter" name="GAP Fingerprinter" version="0.2">
    <description>provides binary fingerprints for glycans using RINGS fingerprinter tool</description>
    <requirements>
        <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
    </requirements> 
    <command interpreter="python"><![CDATA[post_fingerprinter.py -i $input -o $output -d $dendrogram -f $format -g $glycanfragmentsize -s $fingerprintsize -n $folds -c $tanimoto -u $showunit -r $showgroup -m $showsimmatrix -l $showdissimmatrix -e $showmode ]]></command>
    <inputs>
        <param format="kcf" name="input" type="data"  label="KCF source file"/>


 <param name="format" type="integer" value="0" min="0" max="1" label="KCF(0) or Fingerprint(1) format"/>
 <param name="glycanfragmentsize" type="integer" value="10000" min="0" max="100000" label="Glycan fragment size"/>
 <param name="fingerprintsize" type="integer" value="1024" min="1" max="10000" label="Fingerprint size"/>
 <param name="folds" type="integer" value="0" min="0" max="100" label="Number of Folds"/>
 <param name="tanimoto" type="integer" value="1" min="1" max="2" label="Tanimoto(1) or Mod Tanimoto(2)"/>
 <param name="showunit" type="integer" value="0" min="0" max="1" label="Show unit fingerprint"/>
 <param name="showgroup" type="integer" value="0" min="0" max="1" label="Show group fingerprint"/>
 <param name="showsimmatrix" type="integer" value="1" min="0" max="1" label="Show similarity matrix"/>
 <param name="showdissimmatrix" type="integer" value="0" min="0" max="1" label="Show dissimilarity matrix"/>
 <param name="showmode" type="integer" value="0" min="0" max="1" label="Show mode"/>
    </inputs>
    <outputs>
        <data format="html" name="output" label="Fingerprint of $input.name"/>
        <data format="txt" name="dendrogram" label="Newick-like Fingerprint of $input.name"/>
    </outputs>
 <citations>
     <!--  -->
     <citation type="doi">10.1089/omi.2009.0129</citation>
</citations>


    <help> <![CDATA[ 
.. class:: infomark

**What this tool does**

This tool reads KCF glycans and uses the RINGS fingerprint to provide a linear binary based fingerprint based on the motifs found in the glycan.

.. class:: infomark

**Input**

Any KCF glycan or glycan fingerprint (specific to this tool).

.. class:: infomark

**Output**

Html output and a Newick-like linear tree format. 

.. class:: infomark

**Example Input**

Query sequence::

 ENTRY       G00015                      Glycan
 NODE        8
             1   Asn        20     0
             2   GlcNAc     12     0
             3   GlcNAc      3     0
             4   Man        -5     0
             5   Man       -12     5
             6   Man       -12    -5
             7   GlcNAc    -20     5
             8   GlcNAc    -20    -5
 EDGE        7
             1     2:b1    1
             2     3:b1    2:4
             3     4:b1    3:4
             4     5:a1    4:6
             5     6:a1    4:3
             6     7:b1    5:2
             7     8:b1    6:2
 ///
 ENTRY       G00016                      Glycan
 NODE        9
             1   Asn        20     3
             2   GlcNAc     12     3
             3   LFuc        4     8
             4   GlcNAc      3    -2
             5   Man        -5    -2
             6   Man       -12     3
             7   Man       -12    -7
             8   GlcNAc    -20     3
             9   GlcNAc    -20    -7
 EDGE        8
             1     2:b1    1
             2     3:a1    2:6
             3     4:b1    2:4
             4     5:b1    4:4
             5     6:a1    5:6
             6     7:a1    5:3
             7     8:b1    6:2
             8     9:b1    7:2
 ///
 ENTRY       G00017                      Glycan
 NODE        11
             1   Asn        24     3
             2   GlcNAc     14     3
             3   LFuc        7     8
             4   GlcNAc      6    -2
             5   Man        -2    -2
             6   Man        -8     3
             7   Man        -8    -7
             8   GlcNAc    -16     3
             9   GlcNAc    -16    -7
             10  Gal       -24     3
             11  Gal       -24    -7
 EDGE        10
             1     2:b1    1
             2     3:a1    2:6
             3     4:b1    2:4
             4     5:b1    4:4
             5     6:a1    5:6
             6     7:a1    5:3
             7     8:b1    6:2
             8     9:b1    7:2
             9    10:b1    8:4
             10   11:b1    9:4
 ///
 ENTRY       G00018                      Glycan
 NODE        13
             1   Asn        28     3
             2   GlcNAc     18     3
             3   LFuc       10     8
             4   GlcNAc      9    -2
             5   Man         1    -2
             6   Man        -5     4
             7   Man        -5    -8
             8   GlcNAc    -13     4
             9   GlcNAc    -13    -8
             10  Gal       -21     4
             11  Gal       -21    -8
             12  Neu5Ac    -29     4
             13  Neu5Ac    -29    -8
 EDGE        12
             1     2:b1    1
             2     3:a1    2:6
             3     4:b1    2:4
             4     5:b1    4:4
             5     6:a1    5:6
             6     7:a1    5:3
             7     8:b1    6:2
             8     9:b1    7:2
             9    10:b1    8:4
             10   11:b1    9:4
             11   12:a2   10:6
             12   13:a2   11:6
 ///
 ENTRY       G00019                      Glycan
 NODE        9
             1   Asn        20     0
             2   GlcNAc     12     0
             3   GlcNAc      3     0
             4   Man        -5     0
             5   Man       -12     5
             6   Man       -12    -5
             7   GlcNAc    -15     0
             8   GlcNAc    -20     5
             9   GlcNAc    -20    -5
 EDGE        8
             1     2:b1    1
             2     3:b1    2:4
             3     4:b1    3:4
             4     5:a1    4:6
             5     6:a1    4:3
             6     7:b1    4:4
             7     8:b1    5:2
             8     9:b1    6:2
 ///
 ENTRY       G00020                      Glycan
 NODE        9
             1   Asn        20     3
             2   GlcNAc     11     3
             3   GlcNAc      2     3
             4   Man        -6     3
             5   Man       -13     9
             6   Man       -13    -3
             7   GlcNAc    -21     9
             8   GlcNAc    -21     2
             9   GlcNAc    -21    -8
 EDGE        8
             1     2:b1    1
             2     3:b1    2:4
             3     4:b1    3:4
             4     5:a1    4:6
             5     6:a1    4:3
             6     7:b1    5:2
             7     8:b1    6:4
             8     9:b1    6:2
 ///

.. class:: infomark

**Example Output**

The html output varies dependent on options. To see the fingerprints set show unit to 1
example output dendrogram sequence::

 |||G00015_G00016|_|G00019_G00020||_|G00017_G00018||

]]>
    </help>

</tool>