Mercurial > repos > iuc > presto_filterseq
diff presto_filterseq.xml @ 0:7b102129b1e8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
| author | iuc |
|---|---|
| date | Wed, 30 May 2018 15:36:41 -0400 |
| parents | |
| children | 85d929281435 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/presto_filterseq.xml Wed May 30 15:36:41 2018 -0400 @@ -0,0 +1,127 @@ +<tool id="presto_filterseq" name="pRESTO FilterSeq" version="@PRESTO_VERSION@"> + <description>Filters and/or masks reads based on length, quality, missing bases and repeats.</description> + + <macros> + <import>presto_macros.xml</import> + </macros> + + <expand macro="requirements"/> + + <version_command>FilterSeq.py --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$fastq_in' in.fastq && + FilterSeq.py '$cc.command' + --nproc "\${GALAXY_SLOTS:-1}" + -s in.fastq + #if $varExists('cc.q') + -q '$cc.q' + #end if + #if $getVar('cc.inner', False) + --inner + #end if + #if $varExists('cc.win') + --win '$cc.win' + #end if + #if $getVar('cc.reverse', False) + --reverse + #end if + #if $varExists('cc.n') + -n '$cc.n' + #end if + --outdir=. + --outname=tmp_filter_seq + #if $capture_log + --log '$log_out' + #end if + && + mv ./tmp_filter_seq_${cc.command}-pass.fastq $fastq_out + ]]></command> + <inputs> + <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file"/> + <conditional name="cc"> + <param name="command" type="select" label="Command"> + <option value="length">Filters reads by length (length)</option> + <option value="missing">Filters reads by N or gap character count (missing)</option> + <option value="repeats">Filters reads by consecutive nucleotide repeats (repeats)</option> + <option value="quality">Filters reads by quality score (quality)</option> + <option value="maskqual">Masks low quality positions (maskqual)</option> + <option value="trimqual">Trims sequences by quality score decay (trimqual)</option> + </param> + <when value="length"> + <param argument="-n" type="integer" value="" label="Minimum Length" help="Discard reads shorter than this number of bases long."/> + </when> + <when value="missing"> + <param argument="-n" type="integer" value="" label="Max Missing" help="Dicard reads with more than this many no-calls or gaps."/> + </when> + <when value="repeats"> + <param argument="-n" type="integer" value="" label="Max Repeat Length" help="Discard reads with simple repeats of this length of longer."/> + </when> + <when value="quality"> + <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/> + <param argument="--inner" type="boolean" value="false" label="End-Trim Ns" help="Exclude Ns at the ends of the reads from calculation."/> + </when> + <when value="maskqual"> + <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/> + </when> + <when value="trimqual"> + <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/> + <param argument="--win" type="integer" value="10" label="Window Size" help="Window size for moving average quality calculation."/> + <param argument="--reverse" type="boolean" value="false" label="Reverse" help="If true trim the start of the reads instead of the ends."/> + </when> + </conditional> + <expand macro="presto-log-param"/> + </inputs> + + <outputs> + <data name="fastq_out" format="fastq"/> + <expand macro="presto-log-output"/> + </outputs> + + <tests> + <test> + <param name="command" value="length"/> + <param name="n" value="299"/> + <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> + <output name="fastq_out" file="presto_filterseq_length_test_out.fastq" sort="true"/> + </test> + <test> + <param name="command" value="missing"/> + <param name="n" value="281"/> + <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> + <output name="fastq_out" file="presto_filterseq_missing_test_out.fastq" sort="true"/> + </test> + <test> + <param name="command" value="repeats"/> + <param name="n" value="8"/> + <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> + <output name="fastq_out" file="presto_filterseq_repeats_test_out.fastq" sort="true"/> + </test> + <test> + <param name="command" value="quality"/> + <param name="q" value="30"/> + <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> + <output name="fastq_out" file="presto_filterseq_quality_test_out.fastq" sort="true"/> + </test> + <test> + <param name="command" value="maskqual"/> + <param name="q" value="30"/> + <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> + <output name="fastq_out" file="presto_filterseq_maskqual_test_out.fastq" sort="true"/> + </test> + <test> + <param name="command" value="trimqual"/> + <param name="q" value="30"/> + <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> + <output name="fastq_out" file="presto_filterseq_trimqual_test_out.fastq" sort="true"/> + </test> + </tests> + + <help><![CDATA[ +Filters and/or masks reads based on length, quality, missing bases and repeats. + +See the `pRESTO online help <@PRESTO_URL_BASE@/FilterSeq.html>`_ for more information. + +@HELP_NOTE@ + ]]></help> + <expand macro="citations" /> +</tool>