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make native test output smaller than 43MB. Eeesh.
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fubar2 committed Jul 13, 2024
1 parent 245c796 commit 6d6b0fc
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17 changes: 11 additions & 6 deletions tools/microsatbed/microsatbed.xml
Original file line number Diff line number Diff line change
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<param name="mode" type="select" label="Select patterns by motif length; or provide a specific motif pattern to report?" help="Choose *By length:* or *By pattern:* to configure STR selection mode">
<option selected="True" value="ALL">By length: Report all motifs of one or more specified lengths (1-6nt) as bed features</option>
<option value="SPECIFIC">By motif: Report one or more specific motifs (such as TCA,GC) as bed features</option>
<option value="NATIVE">By pytrf findstr: Native command line call to create csv, tsv or gtf output formats</option>
<option value="NATIVE">All exact STR: use the pytrf findstr native command to a create csv, tsv or gtf output</option>
</param>
<when value="ALL">
<param name="subset" type="select" multiple="true" optional="false" label="Select at least 1 specific motif length to report"
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<test expect_num_outputs="1">
<conditional name="reference_genome">
<param name="genome_type_select" value="history"/>
<param name="fasta" value="humsamp.fa"/>
<param name="fasta" value="mouse.fa"/>
</conditional>
<conditional name="mode_cond">
<param name="mode" value="NATIVE"/>
<param name="outformat" value="gff"/>
<param name="minreps" value="2"/>
<param name="monomin" value="20"/>
<param name="dimin" value="10"/>
<param name="trimin" value="5"/>
<param name="tetramin" value="4"/>
<param name="pentamin" value="4"/>
<param name="hexamin" value="2"/>
</conditional>
<output name="bed" value="nativegff_sample" compare="diff" lines_diff="0"/>
</test>
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to uppercase, to prevent them being reported as distinct motifs.
**Filter motifs by length**
**Select motifs by length**
The default tool form setting is to select all dimer motif patterns.
Additional motif lengths from 1 to 6nt can be selected in the multiple-select drop-down list. All features will be returned in a single bed file. For each selected motif length,
the minimum number of repeats required for reporting can be adjusted. **Tandem repeats** are defined as at least 2 of any pattern. This tool allows singleton motifs to be reported,
so is not restricted to short tandem repeats (STR)
**Filter motifs by pattern**
**Select motifs by pattern**
This option allows a motif pattern to be specified as a text string such as *CG* or *ATC*. Multiple motifs can be specified as a comma separated string such as *CG,ATC*.
All features will be returned as a single bed file.
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For example, technical sequencing read bias may be influenced by the density of specific dimers, whether they are repeated or not
such as in https://github.com/arangrhie/T2T-Polish/tree/master/pattern
**Run pytrf findstr to create a csv, tsv or gff format output with all perfect STR**
**Select all perfect STR using pytrf findstr in csv, tsv or gff output format**
This selection runs the pytrf *findstr* option to create gff/csv/tsv outputs as described at the end of https://pytrf.readthedocs.io/en/latest/.
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