/tools/next_gen_conversion/solid_to_fastq.xml

  1<tool id="solid_to_fastq" name="SOLiD-to-FASTQ" version="1.0.0">
  2  <description>converts SOLiD data to FASTQ data</description>
  3  <command interpreter="python">
  4    solid_to_fastq.py 
  5    --input1=$input1 
  6    --input2=$input2
  7    #if $paired.pairedSingle == "single":
  8     --input3="None"
  9     --input4="None"
 10    #else:
 11     --input3=$input3
 12     --input4=$input4
 13    #end if
 14    --output1=$output1
 15    #if $paired.pairedSingle == "single":
 16     --output2="None"
 17    #else:
 18     --output2=$output2
 19    #end if
 20  </command>
 21  <inputs>
 22    <conditional name="paired">
 23      <param name="pairedSingle" type="select" label="Is this library mate-paired?">
 24        <option value="single">Single</option>
 25        <option value="paired">Paired</option>
 26      </param>
 27      <when value="single">
 28        <param name="input1" type="data" format="csfasta" label="F3 read file" />
 29        <param name="input2" type="data" format="qualsolid" label="F3 qual file" />
 30      </when>
 31      <when value="paired">
 32        <param name="input1" type="data" format="csfasta" label="F3 read file" />
 33        <param name="input2" type="data" format="qualsolid" label="F3 qual file" />
 34        <param name="input3" type="data" format="csfasta" label="R3 read file" />
 35        <param name="input4" type="data" format="qualsolid" label="R3 qual file" />      
 36      </when>
 37    </conditional>
 38  </inputs>
 39  <outputs>
 40    <!-- Variable number of outputs. Either one (for single-end) or two (for paired-end) -->
 41    <data name="output1" format="fastqsanger"/>
 42    <data name="output2" format="fastqsanger">
 43      <filter>paired['pairedSingle'] == 'paired'</filter>
 44    </data>    
 45  </outputs>
 46  <tests>
 47    <test>
 48      <param name="pairedSingle" value="single" />
 49      <param name="input1" value="s2fq_phiX.csfasta" ftype="csfasta" />
 50      <param name="input2" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
 51      <output name="output1" file="s2fq_out1.fastqsanger" />
 52    </test>
 53    <test>
 54      <param name="pairedSingle" value="paired" />
 55      <param name="input1" value="s2fq_paired_F3.csfasta" ftype="csfasta" />
 56      <param name="input2" value="s2fq_paired_F3_QV.qualsolid" ftype="qualsolid" />
 57      <param name="input3" value="s2fq_paired_R3.csfasta" ftype="csfasta" />
 58      <param name="input4" value="s2fq_paired_R3_QV.qualsolid" ftype="qualsolid" />
 59      <output name="output1" file="s2fq_out2.fastqsanger" />
 60      <!-- testing framework does not deal with multiple outputs yet
 61      <output name="output2" file="s2fq_out3.fastqsanger" />
 62      -->
 63    </test>
 64  </tests>
 65  <help>
 66
 67**What it does**
 68
 69This tool takes reads and quality files and converts them to FASTQ data ( Sanger variant ). Any -1 qualities are converted to 1 before being converted to FASTQ. Note that it also converts sequences to base pairs.
 70
 71-----
 72
 73**Example**
 74
 75- Converting the following sequences::
 76
 77    >1831_573_1004_F3
 78    T00030133312212111300011021310132222
 79    >1831_573_1567_F3
 80    T03330322230322112131010221102122113
 81
 82- and quality scores::
 83
 84    >1831_573_1004_F3
 85    4 29 34 34 32 32 24 24 20 17 10 34 29 20 34 13 30 34 22 24 11 28 19 17 34 17 24 17 25 34 7 24 14 12 22
 86    >1831_573_1567_F3
 87    8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 32 10 13 6 32 10 6 16 11
 88
 89- will produce the following Sanger FASTQ data::
 90
 91    @1831_573_1004/1
 92    AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
 93    +
 94    >CCAA9952+C>5C.?C79,=42C292:C(9/-7
 95    @1831_573_1567/1
 96    TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
 97    +
 98    ;@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
 99
100    </help>
101</tool>