<tool id="shrimp_color_wrapper" name="SHRiMP for Color-space" version="1.0.0">
  <description>reads mapping against reference sequence </description>
  <command interpreter="python">
    #if $param.skip_or_full=="skip" #shrimp_color_wrapper.py $input_target $input_query $output1 
    #else                           #shrimp_color_wrapper.py $input_target $input_query $output1 $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_crossover_penalty $param.sw_full_hit_threshold $param.sw_vector_hit_threshold  
    #end if#
  </command>
    <inputs>
        <page>
        <param name="input_query" type="data" format="csfasta" label="Align sequencing reads" help="No dataset? Read tip below"/>
        <param name="input_target" type="data" format="fasta" label="against reference" />
        <conditional name="param">
            <param name="skip_or_full" type="select" label="SHRiMP settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List">
                <option value="skip">Commonly used</option>
                <option value="full">Full Parameter List</option>
            </param>
            <when value="skip" />
            <when value="full">
                <param name="spaced_seed"                   type="text"     size="30"   value="1111001111"    label="Spaced Seed" />
                <param name="seed_matches_per_window"       type="integer"  size="5"    value="2"               label="Seed Matches per Window" />
                <param name="seed_hit_taboo_length"         type="integer"  size="5"    value="4"               label="Seed Hit Taboo Length" />
                <param name="seed_generation_taboo_length"  type="integer"  size="5"    value="0"               label="Seed Generation Taboo Length" />
                <param name="seed_window_length"            type="float"    size="10"   value="115.0"           label="Seed Window Length"          help="in percentage"/>
                <param name="max_hits_per_read"             type="integer"  size="10"   value="100"             label="Maximum Hits per Read" />
                <param name="max_read_length"               type="integer"  size="10"   value="1000"            label="Maximum Read Length" />
                <param name="kmer"                          type="integer"  size="10"   value="-1"              label="Kmer Std. Deviation Limit"   help="-1 as None"/>
                <param name="sw_match_value"                type="integer"  size="10"   value="100"             label="S-W Match Value" />
                <param name="sw_mismatch_value"             type="integer"  size="10"   value="-150"            label="S-W Mismatch Value" />
                <param name="sw_gap_open_ref"               type="integer"  size="10"   value="-400"            label="S-W Gap Open Penalty (Reference)" />
                <param name="sw_gap_open_query"             type="integer"  size="10"   value="-400"            label="S-W Gap Open Penalty (Query)" />
                <param name="sw_gap_ext_ref"                type="integer"  size="10"   value="-70"             label="S-W Gap Extend Penalty (Reference)" />
                <param name="sw_gap_ext_query"              type="integer"  size="10"   value="-70"             label="S-W Gap Extend Penalty (Query)" />
                <param name="sw_crossover_penalty"          type="integer"  size="10"   value="-140"            label="S-W Crossover Penalty" />               
                <param name="sw_full_hit_threshold"         type="float"    size="10"   value="68.0"            label="S-W Full Hit Threshold"      help="in percentage"/>
                <param name="sw_vector_hit_threshold"       type="float"    size="10"   value="60.0"            label="S-W Vector Hit Threshold"    help="in percentage"/>
            </when>
        </conditional>
        </page>
    </inputs>
    <outputs>
        <data name="output1" format="tabular"/>
    </outputs>
    <requirements>
      <requirement type="binary">rmapper-cs</requirement>
    </requirements>
    <tests>
        <test>
            <param name="skip_or_full" value="skip" />
            <param name="input_target" value="Ssuis.fasta" ftype="fasta" />
            <param name="input_query" value="shrimp_cs_test1.csfasta" ftype="csfasta"/>
            <output name="output1" file="shrimp_cs_test1.out" />
        </test>
    </tests>
<help>
    
.. class:: warningmark 

To use this tool your dataset needs to be in the *csfasta* (as ABI SOLiD color-space sequences) format. Click pencil icon next to your dataset to set the datatype to *csfasta*.   


-----
    
**What it does**
 
SHRiMP (SHort Read Mapping Package) is a software package for aligning genomic reads against a target genome.  
  

-----

**Input formats**

A multiple color-space file, for example::

    >2_263_779_F3
    T132032030200202202003211302222202230022110222


-----

**Outputs**

The tool returns the default SHRiMP output::

 
     1                      2               3         4        5        6       7      8      9      10
  --------------------------------------------------------------------------------------------------------------------
    >2_263_779_F3   Streptococcus_suis      +       814344  814388      1      45      45    3660    8x19x3x2x6x4x3  

where::

  1. (>2_263_779_F3)        - Read id 
  2. (Streptococcus_suis)   - Reference sequence id
  3. (+)                    - Strand of the read
  4. (814344)               - Start position of the alignment in the reference
  5. (814388)               - End position of the alignment in the reference
  6. (1)                    - Start position of the alignment in the read
  7. (45)                   - End position of the alignment in the read
  8. (45)                   - Length of the read
  9. (3660)                 - Score 
 10. (8x19x3x2x6x4x3)       - Edit string

 
-----

**SHRiMP parameter list**

The commonly used parameters with default value setting::

    -s    Spaced Seed                             (default: 111111011111)
          The spaced seed is a single contiguous string of 0's and 1's. 
          0's represent wildcards, or positions which will always be 
          considered as matching, whereas 1's dictate positions that 
          must match. A string of all 1's will result in a simple kmer scan.
    -n    Seed Matches per Window                 (default: 2)
          The number of seed matches per window dictates how many seeds 
          must match within some window length of the genome before that 
          region is considered for Smith-Waterman alignment. A lower 
          value will increase sensitivity while drastically increasing 
          running time. Higher values will have the opposite effect.
    -t    Seed Hit Taboo Length                   (default: 4)
          The seed taboo length specifies how many target genome bases 
          or colours must exist prior to a previous seed match in order 
          to count another seed match as a hit.
    -9    Seed Generation Taboo Length            (default: 0)
          
    -w    Seed Window Length                      (default: 115.00%)
          This parameter specifies the genomic span in bases (or colours) 
          in which *seed_matches_per_window* must exist before the read 
          is given consideration by the Simth-Waterman alignment machinery.
    -o    Maximum Hits per Read                   (default: 100)
          This parameter specifies how many hits to remember for each read. 
          If more hits are encountered, ones with lower scores are dropped 
          to make room.
    -r    Maximum Read Length                     (default: 1000)
          This parameter specifies the maximum length of reads that will 
          be encountered in the dataset. If larger reads than the default 
          are used, an appropriate value must be passed to *rmapper*.
    -d    Kmer Std. Deviation Limit               (default: -1 [None])
          This option permits pruning read kmers, which occur with 
          frequencies greater than *kmer_std_dev_limit* standard 
          deviations above the average. This can shorten running 
          time at the cost of some sensitivity. 
          *Note*: A negative value disables this option.            
    -m    S-W Match Value                         (default: 100)
          The value applied to matches during the Smith-Waterman score calculation.
    -i    S-W Mismatch Value                      (default: -150)
          The value applied to mismatches during the Smith-Waterman 
          score calculation.
    -g    S-W Gap Open Penalty (Reference)        (default: -400)
          The value applied to gap opens along the reference sequence 
          during the Smith-Waterman score calculation.
          *Note*: Note that for backward compatibility, if -g is set 
          and -q is not set, the gap open penalty for the query will 
          be set to the same value as specified for the reference.
    -q    S-W Gap Open Penalty (Query)            (default: -400)
          The value applied to gap opens along the query sequence during 
          the Smith-Waterman score calculation.        
    -e    S-W Gap Extend Penalty (Reference)      (default: -70)
          The value applied to gap extends during the Smith-Waterman score calculation.
          *Note*: Note that for backward compatibility, if -e is set 
          and -f is not set, the gap exten penalty for the query will 
          be set to the same value as specified for the reference. 
    -f    S-W Gap Extend Penalty (Query)          (default: -70)
          The value applied to gap extends during the Smith-Waterman score calculation.
    -x
    -h    S-W Full Hit Threshold                  (default: 68.00%)
          In letter-space, this parameter determines the threshold 
          score for both vectored and full Smith-Waterman alignments. 
          Any values less than this quantity will be thrown away.
          *Note* This option differs slightly in meaning between letter-space and color-space.
    -v
    

-----

**Reference**
 
 **SHRiMP**: Stephen M. Rumble, Michael Brudno, Phil Lacroute, Vladimir Yanovsky, Marc Fiume, Adrian Dalca. shrimp at cs dot toronto dot edu. 

</help>
</tool>