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comparison lastz.xml @ 12:48d39ee9eb30 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595
author iuc
date Thu, 22 Jan 2026 18:28:16 +0000
parents 37b497aa133f
children
comparison
equal deleted inserted replaced
11:37b497aa133f 12:48d39ee9eb30
257 --format=general- 257 --format=general-
258 #elif str( $output_format.out.format ) == "maf": 258 #elif str( $output_format.out.format ) == "maf":
259 '--format=${output_format.out.maf_type}' 259 '--format=${output_format.out.maf_type}'
260 #elif str( $output_format.out.format ) == "blastn": 260 #elif str( $output_format.out.format ) == "blastn":
261 --format=BLASTN- 261 --format=BLASTN-
262 #elif str( $output_format.out.format ) == "paf":
263 --format=PAF-
262 #elif str( $output_format.out.format ) == "general_full": 264 #elif str( $output_format.out.format ) == "general_full":
263 '--format=general-:${output_format.out.fields}' 265 '--format=general-:${output_format.out.fields}'
264 #elif str( $output_format.out.format ) == "differences": 266 #elif str( $output_format.out.format ) == "differences":
265 '--format=differences' 267 '--format=differences'
266 #end if 268 #end if
498 <option value="bam" selected="true">BAM --format=sam)</option> 500 <option value="bam" selected="true">BAM --format=sam)</option>
499 <option value="general_def">General default (--format=general)</option> 501 <option value="general_def">General default (--format=general)</option>
500 <option value="general_full">Customized general (--format=general[:fields])</option> 502 <option value="general_full">Customized general (--format=general[:fields])</option>
501 <option value="maf">MAF (--format=maf)</option> 503 <option value="maf">MAF (--format=maf)</option>
502 <option value="blastn">blastn (--format=BLASTN)</option> 504 <option value="blastn">blastn (--format=BLASTN)</option>
505 <option value="paf">paf (--format=PAF)</option>
503 <option value="differences">Differences (--format=differences)</option> 506 <option value="differences">Differences (--format=differences)</option>
504 </param> 507 </param>
505 <when value="bam"> 508 <when value="bam">
506 <param name="bam_options" type="select" display="radio" argument="--format=sam, --format=softsam" label="Select a BAM flavor to output" help="Lastz actually outputs SAM data but Galaxy converts it into BAM to save space. For alignments that don't reach the end of a query, ‑‑format=sam uses 'hard clipping', while ‑‑format=softsam uses 'soft clipping'. See the section on 'clipped alignment' in the SAM specification for an explanation of what this means. The options ‑‑format=sam- and ‑‑format=softsam- suppress the SAM header lines. This makes them suitable for concatenating output from multiple runs. If you need to specify readgroup information: use AddOrEplaceReadGroups from Picard package"> 509 <param name="bam_options" type="select" display="radio" argument="--format=sam, --format=softsam" label="Select a BAM flavor to output" help="Lastz actually outputs SAM data but Galaxy converts it into BAM to save space. For alignments that don't reach the end of a query, ‑‑format=sam uses 'hard clipping', while ‑‑format=softsam uses 'soft clipping'. See the section on 'clipped alignment' in the SAM specification for an explanation of what this means. The options ‑‑format=sam- and ‑‑format=softsam- suppress the SAM header lines. This makes them suitable for concatenating output from multiple runs. If you need to specify readgroup information: use AddOrEplaceReadGroups from Picard package">
507 <option value="sam" selected="true">BAM</option> 510 <option value="sam" selected="true">BAM</option>
574 </param> 577 </param>
575 </when> 578 </when>
576 <when value="blastn"> 579 <when value="blastn">
577 <!-- Do nothing --> 580 <!-- Do nothing -->
578 </when> 581 </when>
582 <when value="paf">
583 <!-- Do nothing -->
584 </when>
579 <when value="differences"> 585 <when value="differences">
580 <!-- Do nothing --> 586 <!-- Do nothing -->
581 </when> 587 </when>
582 </conditional> 588 </conditional>
583 <param name="rplot" type="boolean" truevalue="--rdotplot=plot.r" falsevalue="" checked="false" argument="--rdotplot" label="Create a dotplot representation of alignments?" help="The dotplot is only useful if query and target contain exactly one sequence each"/> 589 <param name="rplot" type="boolean" truevalue="--rdotplot=plot.r" falsevalue="" checked="false" argument="--rdotplot" label="Create a dotplot representation of alignments?" help="The dotplot is only useful if query and target contain exactly one sequence each"/>
584 </section> 590 </section>
585 </inputs> 591 </inputs>
586 <outputs> 592 <outputs>
587 <data format="tabular" name="output" label="${tool.name} on ${on_string}: mapped reads"> 593 <data format="tabular" name="output" label="${tool.name} on ${on_string}: mapped reads">
588 <change_format> 594 <change_format>
595 <when input="output_format.out.format" value="paf" format="paf" />
589 <when input="output_format.out.format" value="bam" format="bam" /> 596 <when input="output_format.out.format" value="bam" format="bam" />
590 <when input="output_format.out.format" value="maf" format="maf" /> 597 <when input="output_format.out.format" value="maf" format="maf" />
591 <when input="output_format.out.format" value="differences" format="interval" /> 598 <when input="output_format.out.format" value="differences" format="interval" />
592 </change_format> 599 </change_format>
593 </data> 600 </data>