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/tools/next_gen_conversion/solid2fastq.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1<tool id="solid2fastq" name="Convert">
  2  <description>SOLiD output to fastq</description>
  3  <command interpreter="python">
  4    #if   $is_run.paired == "no"    #solid2fastq.py --fr=$input1 --fq=$input2 --fout=$out_file1 -q $qual $trim_name $trim_first_base $double_encode
  5    #elif $is_run.paired == "yes"   #solid2fastq.py --fr=$input1 --fq=$input2 --fout=$out_file1 --rr=$input3 --rq=$input4 --rout=$out_file2 -q $qual $trim_name $trim_first_base $double_encode
  6    #end if#
  7  </command>
  8  <inputs>
  9    <param name="input1" type="data" format="csfasta" label="Select reads"/>
 10    <param name="input2" type="data" format="qualsolid" label="Select qualities"/>
 11    <conditional name="is_run">
 12        <param name="paired" type="select" label="Is this a mate-pair run?">
 13            <option value="no" selected="true">No</option>
 14            <option value="yes">Yes</option>
 15        </param>
 16        <when value="yes">
 17            <param name="input3" type="data" format="csfasta" label="Select Reverse reads"/>
 18            <param name="input4" type="data" format="qualsolid" label="Select Reverse qualities"/>
 19        </when>
 20        <when value="no">
 21        </when>
 22    </conditional>
 23    <param name="qual" label="Remove reads containing color qualities below this value" type="integer" value="0"/>
 24    <param name="trim_name" type="select" label="Trim trailing &quot;_F3&quot; and &quot;_R3&quot; ?">
 25        <option value="-t" selected="true">Yes</option>
 26        <option value="">No</option>
 27    </param>
 28    <param name="trim_first_base" type="select" label="Trim first base?">
 29        <option value="-f">Yes (BWA)</option>
 30        <option value="" selected="true">No (bowtie)</option>
 31    </param>
 32    <param name="double_encode" type="select" label="Double encode?">
 33        <option value="-d">Yes (BWA)</option>
 34        <option value="" selected="true">No (bowtie)</option>
 35    </param>
 36  </inputs>
 37  <outputs>
 38    <data format="fastqcssanger" name="out_file1"/>
 39    <data format="fastqcssanger" name="out_file2">
 40        <filter>is_run['paired'] == 'yes'</filter>
 41    </data>
 42  </outputs>
 43  <tests>
 44    <test>
 45      <param name="input1" value="fr.csfasta" ftype="csfasta"/>
 46      <param name="input2" value="fr.qualsolid" ftype="qualsolid" />
 47      <param name="paired" value="no"/>
 48      <param name="qual" value="0" />
 49      <param name="trim_first_base" value="No" />
 50      <param name="trim_name" value="No" />
 51      <param name="double_encode" value="No"/>
 52      <output name="out_file1" file="solid2fastq_out_1.fastq"/>
 53    </test>
 54    <test>
 55      <param name="input1" value="fr.csfasta" ftype="csfasta"/>
 56      <param name="input2" value="fr.qualsolid" ftype="qualsolid" />
 57      <param name="paired" value="yes"/>
 58      <param name="input3" value="rr.csfasta" ftype="csfasta"/>
 59      <param name="input4" value="rr.qualsolid" ftype="qualsolid" />
 60      <param name="qual" value="0" />
 61      <param name="trim_first_base" value="No" />
 62      <param name="trim_name" value="Yes" />
 63      <param name="double_encode" value="No"/>
 64      <output name="out_file1" file="solid2fastq_out_2.fastq"/>
 65      <output name="out_file2" file="solid2fastq_out_3.fastq"/>
 66    </test>
 67 </tests>
 68<help>
 69**What it does**
 70
 71Converts output of SOLiD instrument (versions 3.5 and earlier) to fastq format suitable for bowtie, bwa, and PerM mappers.
 72
 73--------
 74
 75**Input datasets**
 76
 77Below are examples of forward (F3) reads and quality scores:
 78
 79Reads::
 80
 81    &gt;1831_573_1004_F3
 82    T00030133312212111300011021310132222
 83    &gt;1831_573_1567_F3
 84    T03330322230322112131010221102122113
 85
 86Quality scores::
 87
 88    &gt;1831_573_1004_F3
 89    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
 90    &gt;1831_573_1567_F3
 91    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
 92
 93
 94**Mate pairs**
 95
 96If your data is from a mate-paired run, you will have additional read and quality datasets that will look similar to the ones above with one exception: the names of reads will be ending with "_R3".
 97In this case choose **Yes** from the *Is this a mate-pair run?* drop down and you will be able to select R reads. When processing mate pairs this tool generates two output files: one for F3 reads and the other for R3 reads.
 98The reads are guaranteed to be paired -- mated reads will be in the same position in F3 and R3 fastq file. However, because pairing is verified it may take a while to process an entire SOLiD run (several hours).
 99
100------
101
102**Explanation of parameters**
103
104**Remove reads containing color qualities below this value** - any read that contains as least one color call with quality lower than the specified value **will not** be reported.
105
106**Trim trailing "_F3" and "_R3"?** - does just that. Not necessary for bowtie. Required for BWA.
107
108**Trim first base?** - SOLiD reads contain an adapter base such as the first T in this read::
109
110    &gt;1831_573_1004_F3
111    T00030133312212111300011021310132222
112  
113this option removes this base leaving only color calls. Not necessary for bowtie. Required for BWA.
114
115**Double encode?** - converts color calls (0123.) to pseudo-nucleotides (ACGTN). Not necessary for bowtie. Required for BWA.
116
117------
118
119**Examples of output**
120
121When all parameters are left "as-is" you will get this (using reads and qualities shown above)::
122
123 @1831_573_1004
124 T00030133312212111300011021310132222
125 +
126 %%&gt;CCAA9952+C&gt;5C.?C79,=42C292:C(9/-7
127 @1831_573_1004
128 T03330322230322112131010221102122113
129 +
130 );@@17?@=&gt;7??@A8?==@4A?A4)A+.'A+'1,
131
132Setting *Trim first base from reads* to **Yes** will produce this::
133
134 @1831_573_1004
135 00030133312212111300011021310132222
136 +
137 %%&gt;CCAA9952+C&gt;5C.?C79,=42C292:C(9/-7
138 @1831_573_1004
139 03330322230322112131010221102122113
140 +
141 );@@17?@=&gt;7??@A8?==@4A?A4)A+.'A+'1,
142
143Finally, setting *Double encode* to **Yes** will yield::
144
145 @1831_573_1004
146 TAAATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
147 +
148 %%&gt;CCAA9952+C&gt;5C.?C79,=42C292:C(9/-7
149 @1831_573_1004
150 TATTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
151 +
152 );@@17?@=&gt;7??@A8?==@4A?A4)A+.'A+'1,
153</help>
154</tool>