Mercurial > repos > devteam > fastq_trimmer_by_quality
diff fastq_trimmer_by_quality.xml @ 4:8b85db5a62e6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
| author | devteam |
|---|---|
| date | Sat, 30 Sep 2017 13:55:01 -0400 |
| parents | 178d14eb7546 |
| children | de3d8685fe42 |
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--- a/fastq_trimmer_by_quality.xml Thu Feb 02 17:03:25 2017 -0500 +++ b/fastq_trimmer_by_quality.xml Sat Sep 30 13:55:01 2017 -0400 @@ -1,130 +1,131 @@ -<tool id="fastq_quality_trimmer" name="FASTQ Quality Trimmer" version="1.0.1"> - <description>by sliding window</description> - <requirements> - <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> - </requirements> - <command>python '$__tool_directory__/fastq_trimmer_by_quality.py' '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s $window_size - -t $step_size -e $trim_ends -a $aggregation_action -x $exclude_count -c '$score_comparison' -q $quality_score - #if $keep_zero_length: - -k - #end if - </command> - <inputs> - <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ File"/> - <param name="keep_zero_length" label="Keep reads with zero length" type="boolean" checked="false"/> - <param name="trim_ends" type="select" label="Trim ends"> - <option value="53" selected="True">5' and 3'</option> - <option value="5">5' only</option> - <option value="3">3' only</option> - </param> - <param name="window_size" type="integer" value="1" label="Window size"/> - <param name="step_size" type="integer" value="1" label="Step Size" /> - <param name="exclude_count" label="Maximum number of bases to exclude from the window during aggregation" value="0" type="integer" /> - <param name="aggregation_action" type="select" label="Aggregate action for window"> - <option value="min" selected="True">min score</option> - <option value="max">max score</option> - <option value="sum">sum of scores</option> - <option value="mean">mean of scores</option> - </param> - <param name="score_comparison" type="select" label="Trim until aggregate score is"> - <sanitizer> - <valid initial="none"> - <add value="<>=!"/> <!-- only allow lt, gt, e, le, ge, ne for this parameter; will be single-quote escaped on commandline --> - </valid> - </sanitizer> - <option value=">">></option> - <option value=">=" selected="true">>=</option> - <option value="==">==</option> - <option value="!=">!=</option> - <option value="<"><</option> - <option value="<="><=</option> - </param> - <param name="quality_score" label="Quality Score" value="0" type="float" /> - </inputs> - <outputs> - <data name="output_file" format_source="input_file" /> - </outputs> - <tests> - <test> - <!-- Trim until window size 1 >= 20;both ends --> - <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> - <param name="keep_zero_length" value="false" /> - <param name="trim_ends" value="53"/> - <param name="window_size" value="1"/> - <param name="step_size" value="1"/> - <param name="exclude_count" value="0"/> - <param name="aggregation_action" value="min"/> - <param name="score_comparison" value=">="/> - <param name="quality_score" value="20"/> - <output name="output_file" file="sanger_full_range_quality_trimmed_out_1.fastqsanger" /> - </test> - <test> - <!-- Trim until window size 1 >= 20; 5' end only --> - <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> - <param name="keep_zero_length" value="false" /> - <param name="trim_ends" value="5"/> - <param name="window_size" value="1"/> - <param name="step_size" value="1"/> - <param name="exclude_count" value="0"/> - <param name="aggregation_action" value="min"/> - <param name="score_comparison" value=">="/> - <param name="quality_score" value="20"/> - <output name="output_file" file="sanger_full_range_quality_trimmed_out_2.fastqsanger" /> - </test> - <test> - <!-- Trim until window size 1 >= 20; 3' end only --> - <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> - <param name="keep_zero_length" value="false" /> - <param name="trim_ends" value="3"/> - <param name="window_size" value="1"/> - <param name="step_size" value="1"/> - <param name="exclude_count" value="0"/> - <param name="aggregation_action" value="min"/> - <param name="score_comparison" value=">="/> - <param name="quality_score" value="20"/> - <output name="output_file" file="sanger_full_range_quality_trimmed_out_3.fastqsanger" /> - </test> - <test> - <!-- Trim until window size 2 >= 1;both ends, 1 deviant score --> - <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> - <param name="keep_zero_length" value="false" /> - <param name="trim_ends" value="53"/> - <param name="window_size" value="2"/> - <param name="step_size" value="1"/> - <param name="exclude_count" value="1"/> - <param name="aggregation_action" value="min"/> - <param name="score_comparison" value=">="/> - <param name="quality_score" value="1"/> - <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> - </test> - <test> - <!-- Trim entire sequences; keep empty reads --> - <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> - <param name="keep_zero_length" value="true" /> - <param name="trim_ends" value="53"/> - <param name="window_size" value="1"/> - <param name="step_size" value="1"/> - <param name="exclude_count" value="0"/> - <param name="aggregation_action" value="min"/> - <param name="score_comparison" value=">="/> - <param name="quality_score" value="999"/> - <output name="output_file" file="sanger_full_range_empty_reads.fastqsanger" /> - </test> - <test> - <!-- Trim entire sequences; discard empty reads --> - <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> - <param name="keep_zero_length" value="false" /> - <param name="trim_ends" value="53"/> - <param name="window_size" value="1"/> - <param name="step_size" value="1"/> - <param name="exclude_count" value="0"/> - <param name="aggregation_action" value="min"/> - <param name="score_comparison" value=">="/> - <param name="quality_score" value="999"/> - <output name="output_file" file="empty_file.dat" /> - </test> - </tests> - <help> +<tool id="fastq_quality_trimmer" name="FASTQ Quality Trimmer" version="1.1.1"> + <description>by sliding window</description> + <requirements> + <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> + </requirements> + <command><![CDATA[ +gx-fastq-trimmer-by-quality '$input_file' '$output_file' -f '${input_file.extension[len('fastq'):]}' -s $window_size +-t $step_size -e $trim_ends -a $aggregation_action -x $exclude_count -c '$score_comparison' -q $quality_score +#if $keep_zero_length: + -k +#end if + ]]></command> + <inputs> + <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ File"/> + <param name="keep_zero_length" type="boolean" checked="false" label="Keep reads with zero length"/> + <param name="trim_ends" type="select" label="Trim ends"> + <option value="53" selected="true">5' and 3'</option> + <option value="5">5' only</option> + <option value="3">3' only</option> + </param> + <param name="window_size" type="integer" value="1" label="Window size"/> + <param name="step_size" type="integer" value="1" label="Step size" /> + <param name="exclude_count" type="integer" value="0" label="Maximum number of bases to exclude from the window during aggregation" /> + <param name="aggregation_action" type="select" label="Aggregate action for window"> + <option value="min" selected="true">min score</option> + <option value="max">max score</option> + <option value="sum">sum of scores</option> + <option value="mean">mean of scores</option> + </param> + <param name="score_comparison" type="select" label="Trim until aggregate score is"> + <sanitizer> + <valid initial="none"> + <add value="<>=!"/> <!-- only allow lt, gt, e, le, ge, ne for this parameter; will be single-quote escaped on commandline --> + </valid> + </sanitizer> + <option value=">">></option> + <option value=">=" selected="true">>=</option> + <option value="==">==</option> + <option value="!=">!=</option> + <option value="<"><</option> + <option value="<="><=</option> + </param> + <param name="quality_score" type="float" value="0" label="Quality score" /> + </inputs> + <outputs> + <data name="output_file" format_source="input_file" /> + </outputs> + <tests> + <!-- Trim until window size 1 >= 20;both ends --> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="keep_zero_length" value="false" /> + <param name="trim_ends" value="53"/> + <param name="window_size" value="1"/> + <param name="step_size" value="1"/> + <param name="exclude_count" value="0"/> + <param name="aggregation_action" value="min"/> + <param name="score_comparison" value=">="/> + <param name="quality_score" value="20"/> + <output name="output_file" file="sanger_full_range_quality_trimmed_out_1.fastqsanger" ftype="fastqsanger" /> + </test> + <!-- Trim until window size 1 >= 20; 5' end only --> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="keep_zero_length" value="false" /> + <param name="trim_ends" value="5"/> + <param name="window_size" value="1"/> + <param name="step_size" value="1"/> + <param name="exclude_count" value="0"/> + <param name="aggregation_action" value="min"/> + <param name="score_comparison" value=">="/> + <param name="quality_score" value="20"/> + <output name="output_file" file="sanger_full_range_quality_trimmed_out_2.fastqsanger" ftype="fastqsanger" /> + </test> + <!-- Trim until window size 1 >= 20; 3' end only --> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="keep_zero_length" value="false" /> + <param name="trim_ends" value="3"/> + <param name="window_size" value="1"/> + <param name="step_size" value="1"/> + <param name="exclude_count" value="0"/> + <param name="aggregation_action" value="min"/> + <param name="score_comparison" value=">="/> + <param name="quality_score" value="20"/> + <output name="output_file" file="sanger_full_range_quality_trimmed_out_3.fastqsanger" ftype="fastqsanger" /> + </test> + <!-- Trim until window size 2 >= 1;both ends, 1 deviant score --> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="keep_zero_length" value="false" /> + <param name="trim_ends" value="53"/> + <param name="window_size" value="2"/> + <param name="step_size" value="1"/> + <param name="exclude_count" value="1"/> + <param name="aggregation_action" value="min"/> + <param name="score_comparison" value=">="/> + <param name="quality_score" value="1"/> + <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + </test> + <!-- Trim entire sequences; keep empty reads --> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="keep_zero_length" value="true" /> + <param name="trim_ends" value="53"/> + <param name="window_size" value="1"/> + <param name="step_size" value="1"/> + <param name="exclude_count" value="0"/> + <param name="aggregation_action" value="min"/> + <param name="score_comparison" value=">="/> + <param name="quality_score" value="999"/> + <output name="output_file" file="sanger_full_range_empty_reads.fastqsanger" ftype="fastqsanger" /> + </test> + <!-- Trim entire sequences; discard empty reads --> + <test> + <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="keep_zero_length" value="false" /> + <param name="trim_ends" value="53"/> + <param name="window_size" value="1"/> + <param name="step_size" value="1"/> + <param name="exclude_count" value="0"/> + <param name="aggregation_action" value="min"/> + <param name="score_comparison" value=">="/> + <param name="quality_score" value="999"/> + <output name="output_file" file="empty_file.dat" ftype="fastqsanger" /> + </test> + </tests> + <help><![CDATA[ **What it does** This tool allows you to trim the ends of reads based upon the aggregate value of quality scores found within a sliding window; a sliding window of size 1 is equivalent to 'simple' trimming of the ends. @@ -138,8 +139,8 @@ .. class:: warningmark Trimming a color space read will cause any adapter base to be lost. - </help> - <citations> - <citation type="doi">10.1093/bioinformatics/btq281</citation> - </citations> + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btq281</citation> + </citations> </tool>