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Wolfgang Maier
d89f0af178
In the previous version, specifying a negative end position would cause a "rotating" behavior of the slice when the reverse index was larger than the length of the string. The fixed version also detects out of range column specifications correctly and should be faster since it uses a set instead of a list lookup and does int conversions up front instead of inside the loop.
144 lines
5.5 KiB
XML
144 lines
5.5 KiB
XML
<tool id="trimmer" name="Trim" version="0.0.2">
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<description>leading or trailing characters</description>
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<requirements>
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<requirement type="package" version="3.8">python</requirement>
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</requirements>
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<command detect_errors="exit_code">
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<![CDATA[
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python '$__tool_directory__/trimmer.py' -a -f '$input1' -c $col -s $start -e $end -i '$ignore' $fastq > '$out_file1'
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]]>
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</command>
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<inputs>
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<param name="input1" type="data" format="tabular,txt" label="Input dataset" />
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<param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" />
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<param name="start" type="integer" value="1" min="1" label="Trim from the beginning up to this position" help="Only positive positions allowed. 1 = do not trim the beginning"/>
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<param name="end" type="integer" value="0" label="Remove everything from this position to the end" help="Use negative position to indicate position starting from the end. 0 = do not trim the end"/>
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<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...). This allows for trimming the seq and qual lines, only if they are not spread over multiple lines (see warning below)">
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<option value="" selected="true">No</option>
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<option value="-q">Yes</option>
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</param>
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<param name="ignore" type="select" display="checkboxes" multiple="true" label="Ignore lines beginning with these characters" help="Lines beginning with these are not trimmed">
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<option value="62">></option>
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<option value="64">@</option>
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<option value="43">+</option>
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<option value="60"><</option>
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<option value="42">*</option>
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<option value="45">-</option>
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<option value="61">=</option>
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<option value="124">|</option>
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<option value="63">?</option>
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<option value="36">$</option>
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<option value="46">.</option>
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<option value="58">:</option>
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<option value="38">&</option>
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<option value="37">%</option>
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<option value="94">^</option>
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<option value="35">#</option>
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</param>
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</inputs>
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<outputs>
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<data name="out_file1" format_source="input1" metadata_source="input1"/>
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</outputs>
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<tests>
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<test>
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<param name="input1" value="trimmer_tab_delimited.dat"/>
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<param name="col" value="0"/>
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<param name="start" value="1"/>
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<param name="end" value="13"/>
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<param name="ignore" value="62"/>
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<param name="fastq" value="No"/>
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<output name="out_file1" file="trimmer_a_f_c0_s1_e13_i62.dat"/>
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</test>
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<test>
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<param name="input1" value="trimmer_tab_delimited.dat"/>
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<param name="col" value="2"/>
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<param name="start" value="1"/>
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<param name="end" value="2"/>
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<param name="ignore" value="62"/>
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<param name="fastq" value="No"/>
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<output name="out_file1" file="trimmer_a_f_c2_s1_e2_i62.dat"/>
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</test>
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<test>
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<param name="input1" value="trimmer_tab_delimited.dat"/>
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<param name="col" value="2"/>
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<param name="start" value="2"/>
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<param name="end" value="-2"/>
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<param name="ignore" value="62"/>
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<param name="fastq" value="No"/>
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<output name="out_file1" file="trimmer_a_f_c2_s2_e-2_i62.dat"/>
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</test>
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</tests>
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<help>
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**What it does**
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Trims specified number of characters from a dataset or a given column (if dataset is tab-delimited).
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-----
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**Example 1**
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Trimming this dataset::
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1234567890
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abcdefghijk
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by setting **Trim from the beginning up to this position** to *2* and **Remove everything from this position to the end** to *6* will produce::
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23456
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bcdef
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-----
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**Example 2**
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Trimming column 2 of this dataset::
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abcde 12345 fghij 67890
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fghij 67890 abcde 12345
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by setting **Trim content of this column only** to *2*, **Trim from the beginning up to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce::
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abcde 234 fghij 67890
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fghij 789 abcde 12345
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-----
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**Example 3**
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Trimming column 2 of this dataset::
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abcde 12345 fghij 67890
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fghij 67890 abcde 12345
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by setting **Trim content of this column only** to *2*, **Trim from the beginning up to this position** to *2*, and **Remove everything from this position to the end** to *-2* will produce::
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abcde 23 fghij 67890
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fghij 78 abcde 12345
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----
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**Trimming FASTQ datasets**
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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::
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@081017-and-081020:1:1:1715:1759
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GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
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+
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II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B
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can be done by setting **Remove everything from this position to the end** to 31::
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@081017-and-081020:1:1:1715:1759
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GGACTCAGATAGTAATCCACGCTCCTTTAAA
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+
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II#IIIIIII$5+.(9IIIIIII$%*$G$A3
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**Note** that headers are skipped.
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.. class:: warningmark
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**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.
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</help>
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</tool>
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