view trimmer.xml @ 1:e632b6c79f7b

Added quotes and brackets to appropriate command arguments

<tool id="trimmer" name="Trim" version="0.0.1">
    <description>leading or trailing characters</description>
    <command interpreter="python">
    trimmer.py -a -f "${input1}" -c "${col}" -s "${start}" -e "${end}" -i "${ignore}" "${fastq}" > "${out_file1}"
    </command>
    <inputs>
        <param format="tabular,txt" name="input1" type="data" label="this dataset"/>
        <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" />
        <param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/>
        <param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/>
        <param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)">
            <option selected="true" value="">No</option>
            <option value="-q">Yes</option>
        </param>
        <param name="ignore" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are not trimmed">
            <option value="62">&gt;</option>
            <option value="64">@</option>
            <option value="43">+</option>
            <option value="60">&lt;</option>
            <option value="42">*</option>
            <option value="45">-</option>
            <option value="61">=</option>
            <option value="124">|</option>
            <option value="63">?</option>
            <option value="36">$</option>
            <option value="46">.</option>
            <option value="58">:</option>
            <option value="38">&amp;</option>
            <option value="37">%</option>
            <option value="94">^</option>
            <option value="35">&#35;</option>
         </param>   
    </inputs>
    <outputs>
        <data name="out_file1" format="input" metadata_source="input1"/>
    </outputs>
    <tests>
        <test>
           <param name="input1" value="trimmer_tab_delimited.dat"/>
           <param name="col" value="0"/>
           <param name="start" value="1"/>
           <param name="end" value="13"/>
           <param name="ignore" value="62"/>
           <param name="fastq" value="No"/>
           <output name="out_file1" file="trimmer_a_f_c0_s1_e13_i62.dat"/>
        </test>
        <test>
           <param name="input1" value="trimmer_tab_delimited.dat"/>
           <param name="col" value="2"/>
           <param name="start" value="1"/>
           <param name="end" value="2"/>
           <param name="ignore" value="62"/>
           <param name="fastq" value="No"/>
           <output name="out_file1" file="trimmer_a_f_c2_s1_e2_i62.dat"/>
        </test>

    </tests>

    <help>


**What it does**

Trims specified number of characters from a dataset or its field (if dataset is tab-delimited).

-----

**Example 1**

Trimming this dataset::

  1234567890
  abcdefghijk

by setting **Trim from the beginning to this position** to *2* and **Remove everything from this position to the end** to *6* will produce::

  23456
  bcdef

-----

**Example 2**

Trimming column 2 of this dataset::

  abcde 12345 fghij 67890
  fghij 67890 abcde 12345

by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce::

  abcde  234 fghij 67890
  fghij  789 abcde 12345

-----

**Trimming FASTQ datasets**

This tool can be used to trim sequences and quality strings in fastq datasets. This is done by selected *Yes* from the **Is input dataset in fastq format?** dropdown. If set to *Yes*, the tool will skip all even numbered lines (see warning below). For example, trimming last 5 bases of this dataset::

  @081017-and-081020:1:1:1715:1759
  GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
  +
  II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&amp;&amp;B
  
cab done by setting **Remove everything from this position to the end** to 31::

  @081017-and-081020:1:1:1715:1759
  GGACTCAGATAGTAATCCACGCTCCTTTAAA
  +
  II#IIIIIII$5+.(9IIIIIII$%*$G$A3 
  
**Note** that headers are skipped.

.. class:: warningmark

**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example.


    </help>
</tool>