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Updated test parameters for tools/bbtools (#6281)
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* Updating tools/bbtools from version 39.06 to 39.08

* fixing test and reformating

* Fixed test parameters

---------

Co-authored-by: planemo-autoupdate <[email protected]>
Co-authored-by: Bjoern Gruening <[email protected]>
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@SaimMomin12 @bgruening
3 people authored Aug 27, 2024
1 parent 329ba03 commit cd59ba2
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31 changes: 15 additions & 16 deletions tools/bbtools/bbduk.xml
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Expand Up @@ -154,11 +154,11 @@ t=\${GALAXY_SLOTS:-4}
</param>
<when value="no_reference"/>
<when value="files">
<param name="reference" type="data" format="fasta,fasta.gz" multiple="true" optional="false" label="Select one or more fasta file"/>
<param name="reference" type="data" format="fasta,fasta.gz" optional="false" label="Select one or more fasta file" multiple="true"/>
<expand macro="ktrim_cond"/>
</when>
<when value="keywords">
<param name="reference" type="select" multiple="true" optional="false" label="Select one or more keywords">
<param name="reference" type="select" optional="false" label="Select one or more keywords" multiple="true">
<option value="adapters">adapters</option>
<option value="artifacts">artifacts</option>
<option value="phix">phix</option>
Expand All @@ -171,34 +171,34 @@ t=\${GALAXY_SLOTS:-4}
</when>
</conditional>
<section name="advanced_options" title="Advanced options" expanded="false">
<param argument="k" type="integer" value="27" min="1" label="Kmer length used for finding contaminants"/>
<param argument="k" type="integer" min="1" value="27" label="Kmer length used for finding contaminants"/>
<param argument="rcomp" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Look for reverse-complements of kmers in addition to forward kmers?"/>
<param argument="maskmiddle" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Treat the middle base of a kmer as a wildcard to increase sensitivity in the presence of errors?"/>
<param argument="minkmerhits" type="integer" value="1" min="1" label="Reads need at least this many matching kmers to be considered as matching the reference"/>
<param argument="minkmerfraction" type="float" value="0" min="0" label="A read needs at least this fraction of its total kmers to hit a ref in order to be considered a match"/>
<param argument="mincovfraction" type="float" value="0" min="0" label="A read needs at least this fraction of its total bases to be covered by ref kmers to be considered a match"/>
<param argument="hammingdistance" type="integer" value="0" min="0" label="Maximum Hamming distance for ref kmers (subs only)"/>
<param argument="qhdist" type="integer" value="0" min="0" label="Hamming distance for query kmers"/>
<param argument="editdistance" type="integer" value="0" min="0" label="Maximum edit distance from ref kmers (subs and indels)"/>
<param argument="minkmerhits" type="integer" min="1" value="1" label="Reads need at least this many matching kmers to be considered as matching the reference"/>
<param argument="minkmerfraction" type="float" min="0" value="0" label="A read needs at least this fraction of its total kmers to hit a ref in order to be considered a match"/>
<param argument="mincovfraction" type="float" min="0" value="0" label="A read needs at least this fraction of its total bases to be covered by ref kmers to be considered a match"/>
<param argument="hammingdistance" type="integer" min="0" value="0" label="Maximum Hamming distance for ref kmers (subs only)"/>
<param argument="qhdist" type="integer" min="0" value="0" label="Hamming distance for query kmers"/>
<param argument="editdistance" type="integer" min="0" value="0" label="Maximum edit distance from ref kmers (subs and indels)"/>
<param argument="forbidn" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Do not match kmers comntaining N?"/>
<param argument="trimfailures" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim failed reads to 1bp instead of discarding them?"/>
<param argument="findbestmatch" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Associate read with sequence sharing most kmers if multiple matches?"/>
<param argument="skipr1" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 1?"/>
<param argument="skipr2" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 2?"/>
</section>
<param name="outputs_select" type="select" multiple="true" optional="false" label="Specify outputs">
<param name="outputs_select" type="select" optional="false" label="Specify outputs" multiple="true">
<option value="outu">Unmatched</option>
<option value="outm">Matched</option>
<option value="outs">Single</option>
</param>
<conditional name="output_stats_cond">
<param name="output_stats" type="select" label="Output statistics?">
<param name="output_stats" type="select" label="Output statistics?">
<option value="no" selected="true">No</option>
<option value="yes">Yes</option>
</param>
<when value="no"/>
<when value="yes">
<param name="output_stats_select" type="select" multiple="true" optional="false" label="Specify statistics outputs">
<param name="output_stats_select" type="select" optional="false" label="Specify statistics outputs" multiple="true">
<option value="stats">Statistics about which contamininants were detected</option>
<option value="ref">Statistics on a per-reference-file basis</option>
<option value="rpkm">RPKM for each reference sequence (for RNA-seq)</option>
Expand All @@ -207,13 +207,13 @@ t=\${GALAXY_SLOTS:-4}
</when>
</conditional>
<conditional name="output_hists_cond">
<param name="output_hists" type="select" label="Output histograms?">
<param name="output_hists" type="select" label="Output histograms?">
<option value="no" selected="true">No</option>
<option value="yes">Yes</option>
</param>
<when value="no"/>
<when value="yes">
<param name="output_hists_select" type="select" multiple="true" optional="false" label="Specify statistics outputs">
<param name="output_hists_select" type="select" optional="false" label="Specify statistics outputs" multiple="true">
<option value="bhist">Base composition histogram by position</option>
<option value="quhist">Quality histogram by position</option>
<option value="quchist">Count of bases with each quality value</option>
Expand All @@ -229,7 +229,7 @@ t=\${GALAXY_SLOTS:-4}
</inputs>
<outputs>
<data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)">
<filter>str(outputs_select).find('outu') >= 0</filter>
<filter>str(outputs_select).find('outu') &gt;= 0</filter>
<filter>'outu' in outputs_select</filter>
</data>
<data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Unmatched)">
Expand Down Expand Up @@ -350,4 +350,3 @@ trimming, kmer masking, or kmer filtering). At most 1 kmer-based operation can b
</help>
<expand macro="citations"/>
</tool>

5 changes: 2 additions & 3 deletions tools/bbtools/bbmap.xml
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Expand Up @@ -202,7 +202,7 @@ renamebyinsert='$output_options.renamebyinsert'
<param argument="untrim" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Undo trimming after mapping?" help="Untrimmed bases will be soft-clipped in cigar strings"/>
<param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
<param argument="mintrimlength" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
<param argument="fakefastaquality" type="integer" value="-1" max="50" label="Set to a positive number 1-50 to generate fake quality strings for fasta input reads"/>
<param argument="fakefastaquality" type="integer" max="50" value="-1" label="Set to a positive number 1-50 to generate fake quality strings for fasta input reads"/>
<param argument="ignorebadquality" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Keep going, rather than crashing, if a read has out-of-range quality values?"/>
<param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
<param argument="minaveragequality" type="integer" value="0" label="Do not map reads with average quality below this value"/>
Expand All @@ -225,7 +225,7 @@ renamebyinsert='$output_options.renamebyinsert'
</param>
</section>
<section name="pf_options" title="Post-filtering options">
<param argument="idfilter" type="integer" value="0" min="0" max="1" label="Specify exact minimum identity allowed for alignments to be output" help="Independent of approximate minimum alignment identity to look for"/>
<param argument="idfilter" type="integer" min="0" max="1" value="0" label="Specify exact minimum identity allowed for alignments to be output" help="Independent of approximate minimum alignment identity to look for"/>
<param argument="subfilter" type="integer" value="-1" label="Ban alignments with more than this many substitutions" help="Negative value ignores"/>
<param argument="insfilter" type="integer" value="-1" label="Ban alignments with more than this many insertions" help="Negative value ignores"/>
<param argument="delfilter" type="integer" value="-1" label="Ban alignments with more than this many deletions" help="Negative value ignores"/>
Expand Down Expand Up @@ -365,4 +365,3 @@ evaluating new sequencing platforms.
</help>
<expand macro="citations"/>
</tool>

7 changes: 0 additions & 7 deletions tools/bbtools/bbmerge.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,6 @@ $merge_options.strictness=t
]]></command>
<inputs>
<expand macro="input_type_cond"/>

<section name="qt_options" title="Quality and trimming options">
<param name="qtrim" type="select" label="Select option for quality trimming ends before mapping">
<option value="f" selected="true">No trimming</option>
Expand All @@ -110,7 +109,6 @@ $merge_options.strictness=t
<param argument="minlength_after_trim" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
<param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
</section>

<section name="merge_options" title="Merging parameters">
<param name="strictness" type="select" label="Select option for quality trimming ends before mapping">
<option value="xstrict">max strict</option>
Expand All @@ -128,16 +126,13 @@ $merge_options.strictness=t
<param argument="trimnonoverlapping" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim all non-overlapping portions, leaving only consensus sequence. By default, only sequence to the right of the overlap (adapter sequence) is trimmed."/>
<param argument="mininsert" type="integer" value="35" label="Minimum insert size to merge reads"/>
<param argument="minoverlap" type="integer" value="12" label="Minimum number of overlapping bases to allow merging"/>

<param argument="minq" type="integer" value="9" label="Ignore bases with quality below this"/>
<param argument="maxq" type="integer" value="41" label="Cap output quality scores at this"/>

<param argument="entropy" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Increase the minimum overlap requirement for low-complexity reads"/>
<param argument="efilter" type="integer" value="6" label="Ban overlaps with over this many times the expected number of errors." help="Lower is more strict, -1 disables."/>
<param argument="pfilter" type="float" value="0.00004" label="Probability filter to disallow improbable overlaps." help="Higher is stricter. 0 will disable the filter; 1 will allow only perfect overlaps."/>
<param argument="kfilter" type="integer" value="41" label="Ban overlaps that create kmers with count below this value" help="Requires good coverage, 0 disables."/>
<param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Take quality factors into account" help="If disabled, quality values are completely ignored, both for overlap detection and filtering. May be useful for data with inaccurate quality values."/>

<conditional name="adapters">
<param name="selector" type="select" label="Provide adapter sequences to improve accuracy?">
<option value="wout_adapters" selected="true">No</option>
Expand All @@ -149,7 +144,6 @@ $merge_options.strictness=t
<param argument="adapter2" type="text" value="" label="Right adapter sequence"/>
</when>
</conditional>

<conditional name="merge_mode">
<param name="selector" type="select" label="Evaluate overlaps via..." help="In the ratio mode, overlaps are decided based on the ratio of matching to mismatching bases. Flat mode scores overlaps based on the total number of mismatching bases only.">
<option value="Ratio mode" selected="true">Ratio mode</option>
Expand Down Expand Up @@ -253,4 +247,3 @@ output.fastq::
</help>
<expand macro="citations"/>
</tool>

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