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comparison lastz.xml @ 9:2ff111fac1d7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c"
author iuc
date Fri, 02 Apr 2021 17:18:40 +0000
parents e7f19d6a9af8
children 3e1ea2facca6
comparison
equal deleted inserted replaced
8:e7f19d6a9af8 9:2ff111fac1d7
1 <tool id="lastz_wrapper_2" name="LASTZ" version="1.3.2"> 1 <tool id="lastz_wrapper_2" name="LASTZ" version="1.3.3">
2 <description>: align long sequences</description> 2 <description>: align long sequences</description>
3 <macros> 3 <macros>
4 <import>lastz_macros.xml</import> 4 <import>lastz_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
253 '--format=${output_format.out.maf_type}' 253 '--format=${output_format.out.maf_type}'
254 #elif str( $output_format.out.format ) == "blastn": 254 #elif str( $output_format.out.format ) == "blastn":
255 --format=BLASTN- 255 --format=BLASTN-
256 #elif str( $output_format.out.format ) == "general_full": 256 #elif str( $output_format.out.format ) == "general_full":
257 '--format=general-:${output_format.out.fields}' 257 '--format=general-:${output_format.out.fields}'
258 #elif str( $output_format.out.format ) == "differences":
259 '--format=differences'
258 #end if 260 #end if
259 --action:target=multiple 261 --action:target=multiple
260 $output_format.rplot 262 $output_format.rplot
261 #if str( $output_format.out.format ) == "bam": 263 #if str( $output_format.out.format ) == "bam":
262 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '${output}' 264 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '${output}'
263 #else: 265 #else:
264 > '${output}' 266 > '${output}'
265 #end if 267 #end if
266 #if $output_format.rplot: 268 #if $output_format.rplot:
267 && 269 &&
490 <option value="bam" selected="true">BAM --format=sam)</option> 492 <option value="bam" selected="true">BAM --format=sam)</option>
491 <option value="general_def">General default (--format=general)</option> 493 <option value="general_def">General default (--format=general)</option>
492 <option value="general_full">Customized general (‑‑format=general[:fields])</option> 494 <option value="general_full">Customized general (‑‑format=general[:fields])</option>
493 <option value="maf">MAF (--format=maf)</option> 495 <option value="maf">MAF (--format=maf)</option>
494 <option value="blastn">blastn (--format=BLASTN)</option> 496 <option value="blastn">blastn (--format=BLASTN)</option>
497 <option value="differences">Differences (--format=differences)</option>
495 </param> 498 </param>
496 <when value="bam"> 499 <when value="bam">
497 <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"> 500 <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">
498 <option value="sam" selected="true">BAM</option> 501 <option value="sam" selected="true">BAM</option>
499 <option value="softsam">soft-clipped BAM</option> 502 <option value="softsam">soft-clipped BAM</option>
565 </param> 568 </param>
566 </when> 569 </when>
567 <when value="blastn"> 570 <when value="blastn">
568 <!-- Do nothing --> 571 <!-- Do nothing -->
569 </when> 572 </when>
573 <when value="differences">
574 <!-- Do nothing -->
575 </when>
570 </conditional> 576 </conditional>
571 <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"/> 577 <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"/>
572 </section> 578 </section>
573 </inputs> 579 </inputs>
574 <outputs> 580 <outputs>
575 <data format="tabular" name="output" label="${tool.name} on ${on_string}: mapped reads"> 581 <data format="tabular" name="output" label="${tool.name} on ${on_string}: mapped reads">
576 <change_format> 582 <change_format>
577 <when input="output_format.out.format" value="bam" format="bam" /> 583 <when input="output_format.out.format" value="bam" format="bam" />
578 <when input="output_format.out.format" value="maf" format="maf" /> 584 <when input="output_format.out.format" value="maf" format="maf" />
585 <when input="output_format.out.format" value="differences" format="interval" />
579 </change_format> 586 </change_format>
580 </data> 587 </data>
581 <data format="png" name="out_plot" label="${tool.name} on ${on_string}: dot plot"> 588 <data format="png" name="out_plot" label="${tool.name} on ${on_string}: dot plot">
582 <filter>output_format['rplot']</filter> 589 <filter>output_format['rplot']</filter>
583 </data> 590 </data>
640 <param name="query" ftype="fastq" value="chrM_mouse.fq" /> 647 <param name="query" ftype="fastq" value="chrM_mouse.fq" />
641 <param name="strand" value="--strand=both" /> 648 <param name="strand" value="--strand=both" />
642 <param name="format" value="blastn" /> 649 <param name="format" value="blastn" />
643 <output name="output" value="test5.out" /> 650 <output name="output" value="test5.out" />
644 </test> 651 </test>
652 <test>
653 <param name="ref_source" value="cached" />
654 <param name="target_2bit" value="phiX174" />
655 <param name="query" value="phiX_split.fasta" />
656 <param name="strand" value="--strand=both" />
657 <param name="format" value="differences" />
658 <output name="output" value="test6.out" />
659 </test>
645 </tests> 660 </tests>
646 661
647 <help><![CDATA[ 662 <help><![CDATA[
648 663
649 **What is does** 664 **What is does**