annotate fastq_to_tabular.xml @ 5:43807a65369f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845

<tool id="fastq_to_tabular" name="FASTQ to Tabular" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <edam_topics>
        <edam_topic>topic_0622</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_0233</edam_operation>
    </edam_operations>
    <expand macro="requirements"/>
    <command><![CDATA[
gx-fastq-to-tabular '$input_file' '$output_file' $descr_columns '${input_file.extension[len('fastq'):]}'
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa,fastqsanger.gz,fastqcssanger.gz,fastqillumina.gz,fastqsolexa.gz,fastqsanger.bz2,fastqcssanger.bz2,fastqillumina.bz2,fastqsolexa.bz2" label="FASTQ file to convert" />
        <param name="descr_columns" type="integer" min="1" value="1" label="How many columns to divide title string into?" help="Typically 2 to take the ID (first word) and decription (rest) as two columns, or 1 to give a single column" />
    </inputs>
    <outputs>
        <data name="output_file" format="tabular" />
    </outputs>
    <tests>
        <!-- basic test -->
        <test>
            <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
            <param name="descr_columns" value="1"/>
            <output name="output_file" file="fastq_to_tabular_out_1.tabular" />
        </test>
        <!-- compression test -->
        <test>
            <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastqsanger.gz" />
            <param name="descr_columns" value="1"/>
            <output name="output_file" file="fastq_to_tabular_out_1.tabular" />
        </test>
        <!-- color space test -->
        <test>
            <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
            <param name="descr_columns" value="1"/>
            <output name="output_file" file="fastq_to_tabular_out_2.tabular" />
        </test>
        <!-- split title into columns -->
        <test>
            <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
            <param name="descr_columns" value="2"/>
            <output name="output_file" file="fastq_to_tabular_out_3.tabular" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool converts FASTQ sequencing reads to a Tabular file.

It is conventional to take the first word of the FASTQ "@" title line as the identifier, and any remaining text to be a free form description.
It is therefore often useful to split this text into two columns in Galaxy (identifier and any description) by setting **How many columns to divide title string into?** to **2**.
In some cases the description can be usefully broken up into more columns -- see the examples .

Tab characters, if present in the source FASTQ title, will be converted to spaces.

-----

**Example**

Consider the following two 454 reads in Sanger FASTQ format (using line wrapping for display, but do note not all tools will accept line wrapped FASTQ files)::

 @FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
 tcagTTAAGATGGGATAATATCCTCAGATTGCGTGATGAACTTTGTTCTGGTGGAGGAGAAGGAAGTGCATTCGACGTAT
 GCCCGTTTGTCGATATTTGtatttaaagtaatccgtcacaaatcagtgacataaatattatttagatttcgggagcaact
 ttatttattccacaagcaggtttaaattttaaatttaaattattgcagaagactttaaattaacctcgttgtcggagtca
 tttgttcggttattggtcgaaagtaaccncgggaagtgccgaaaactaacaaacaaaagaagatagtgaaattttaatta
 aaanaaatagccaaacgtaactaactaaaacggacccgtcgaggaactgccaacggacgacacagggagtagnnn
 +FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] 
 FFFDDDDDDDA666?688FFHGGIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIGHGFFFFF====DFFFFFFFFFFFFFF
 D???:3104/76=:5...4.3,,,366////4<ABBAAA=CCFDDDDDDDD:666CDFFFF=<ABA=;:333111<===9
 9;B889FFFFFFDDBDBDDD=8844231..,,,-,,,,,,,,1133..---17111,,,,,22555131121.--.,333 
 11,.,,3--,,.,,--,3511123..--!,,,,--,----9,,,,8=,,-,,,-,,,,---26:9:5-..1,,,,11//,
 ,,,!,,1917--,,,,-3.,--,,17,,,,---+11113.030000,,,044400036;96662.//;7><;!!!
 @FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
 tcagCCAGCAATTCCGACTTAATTGTTCTTCTTCCATCATTCATCTCGACTAACAGTTCTACGATTAATGAGTTTGGCtt
 taatttgttgttcattattgtcacaattacactactgagactgccaaggcacncagggataggnn
 +FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
 FFFFFFFFFDDDDFFFFGFDDDDBAAAAA=<4444@@B=555:BBBBB@@?8:8<?<89898<84442;==3,,,514,,
 ,11,,,.,,21777555513,..--1115758.//34488><<;;;;9944/!/4,,,57855!!

By default this is converted into a 3 column tabular file, with the full FASTQ title used as column 1:

=================================================================================================== ============== ==============
FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
=================================================================================================== ============== ==============

If you specified the title should be turned into 2 columns, you'd get 4 columns in total:

============== ==================================================================================== ============== ==============
FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
============== ==================================================================================== ============== ==============

Similarly, for this example treating the title string as 7 columns makes sense:

============== ============ ========== =========== ============= ============== =================== ============== ==============
FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
============== ============ ========== =========== ============= ============== =================== ============== ==============

Note the sequences and quality strings have been truncated for display purposes in the above tables.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btq281</citation>
    </citations>
</tool>