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comparison macros.xml @ 5:eca03db4f612 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
author iuc
date Wed, 08 Jan 2020 09:15:19 -0500
parents c237ba772225
children 326a3db8d9d1
comparison
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4:c237ba772225 5:eca03db4f612
1 <macros> 1 <macros>
2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> 2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
3 <token name="@WRAPPER_VERSION@">3.1.1</token> 3 <token name="@WRAPPER_VERSION@">3.2.1</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement> 6 <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement>
7 <!--<requirement type="package" version="3.7">python</requirement>-->
8 <yield /> 7 <yield />
9 </requirements> 8 </requirements>
10 <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command> 9 <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command>
11 </xml> 10 </xml>
12 11
163 <xml name="region"> 162 <xml name="region">
164 <param argument="--region" type="text" label="Region of the genome to limit the operation" 163 <param argument="--region" type="text" label="Region of the genome to limit the operation"
165 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" /> 164 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" />
166 </xml> 165 </xml>
167 166
168 <xml name='matrix_h5_cooler_multiple_macro'> 167 <xml name="matrix_h5_cooler_multiple_macro">
169 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" 168 <param name="matrix_h5_cooler_multiple" type="data" format="h5,cool"
170 label="Matricies to compute on" multiple="true"/> 169 label="Matricies to compute on" multiple="true"/>
171 </xml> 170 </xml>
172 <token name="@REFERENCES@"> 171 <token name="@REFERENCES@">
173 172
174 .. class:: infomark 173 .. class:: infomark
185 .. _help site: https://github.com/deeptools/pyGenomeTracks 184 .. _help site: https://github.com/deeptools/pyGenomeTracks
186 185
187 </token> 186 </token>
188 187
189 <xml name="track_input_bed_macro"> 188 <xml name="track_input_bed_macro">
190 <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple='True'/> 189 <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple="True"/>
191 </xml> 190 </xml>
192 <xml name="track_input_bed_gtf_macro"> 191 <xml name="track_input_bed_gtf_macro">
193 <param name="track_input_bed" type="data" format="bed,gtf" label="Track file bed or gtf format" multiple='True'/> 192 <param name="track_input_bed" type="data" format="bed,gtf" label="Track file bed or gtf format" multiple="True"/>
194 </xml> 193 </xml>
195 <xml name="track_input_narrow_peak_macro"> 194 <xml name="track_input_narrow_peak_macro">
196 <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file encodepeak or format" multiple='True'/> 195 <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file encodepeak or format" multiple="True"/>
197 </xml> 196 </xml>
198 <xml name="track_input_bed_single_macro"> 197 <xml name="track_input_bed_single_macro">
199 <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/> 198 <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/>
200 </xml> 199 </xml>
201 <xml name="track_input_bedgraph_macro"> 200 <xml name="track_input_bedgraph_macro">
202 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" multiple='True'/> 201 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" multiple="True"/>
203 </xml> 202 </xml>
204 <xml name="track_input_bigwig_macro"> 203 <xml name="track_input_bigwig_macro">
205 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" multiple='True'/> 204 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" multiple="True"/>
206 </xml> 205 </xml>
207 <xml name="track_input_bedgraph_matrix_macro"> 206 <xml name="track_input_bedgraph_matrix_macro">
208 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" multiple='True'/> 207 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" multiple="True"/>
208 </xml>
209 <xml name="track_input_link_macro">
210 <param name="track_input_link" type="data" format="bed,interval" label="Track file for links" multiple="False"/>
209 </xml> 211 </xml>
210 <xml name="plot_title"> 212 <xml name="plot_title">
211 <param name="title" type="text" optional="true" label="Plot title" multiple='True'/> 213 <param name="title" type="text" optional="true" label="Plot title" multiple="True"/>
212 </xml> 214 </xml>
213 <xml name="spacer_macro"> 215 <xml name="spacer_macro">
214 <param name="spacer_height" type="float" value="" optional="True" 216 <param name="spacer_height" type="float" value="" optional="True"
215 label="Include spacer at the end of the track" help="Height of the spacer." /> 217 label="Include spacer at the end of the track" help="Height of the spacer." />
216 </xml> 218 </xml>
217 <xml name="inverted_macro"> 219 <xml name="inverted_macro">
218 <param name="invert_orientation" type="boolean" truevalue="yes" falsevalue="no" checked="false" 220 <param name="invert_orientation" type="boolean" truevalue="true" falsevalue="false" checked="false"
219 label="Invert the track" /> 221 label="Invert the track" />
220 </xml> 222 </xml>
221 <xml name="color_bed_macro"> 223 <xml name="color_bed_macro">
222 <conditional name="color_bed"> 224 <conditional name="color_bed">
223 <param name="color_bed_select" type="select" label="Use color:"> 225 <param name="color_bed_select" type="select" label="Use color:">
377 <xml name="color_coverage_macro"> 379 <xml name="color_coverage_macro">
378 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 380 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
379 <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/> 381 <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
380 <conditional name="color_negative"> 382 <conditional name="color_negative">
381 <param name="color_negative_select" type="select" label="Use a different color for negative values"> 383 <param name="color_negative_select" type="select" label="Use a different color for negative values">
382 <option value="no" selected="True">No</option> 384 <option value="false" selected="True">No</option>
383 <option value="yes">Yes</option> 385 <option value="true">Yes</option>
384 </param> 386 </param>
385 <when value="no" /> 387 <when value="false" />
386 <when value="yes"> 388 <when value="true">
387 <param name="color" type="color" value="#000000" label="Color of negative values" optional="True" /> 389 <param name="color" type="color" value="#000000" label="Color of negative values" optional="True" />
388 </when> 390 </when>
389 </conditional> 391 </conditional>
390 </xml> 392 </xml>
391 <xml name="overlay_macro"> 393 <xml name="overlay_macro">
423 <option value="max">max=maximum value</option> 425 <option value="max">max=maximum value</option>
424 <option value="coverage">coverage=number of covered bases</option> 426 <option value="coverage">coverage=number of covered bases</option>
425 <option value="std">std=standard deviation</option> 427 <option value="std">std=standard deviation</option>
426 </param> 428 </param>
427 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" /> 429 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
428 <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false" 430 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
429 label="NAN's to zeros" /> 431 label="NAN's to zeros" />
430 </section> 432 </section>
431 </xml> 433 </xml>
434 <xml name="bed_advanced_macro">
435 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
436 <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false"
437 label="Global max rows" />
438 <param name="gene_rows" type="integer" value="" optional="True" label="Maximum number of gene rows" />
439 <param name="max_labels" type="integer" value="60" label="Maximum number of gene labels to display" />
440 <param name="line_width" type="float" value="0.5" label="width of lines" />
441 <section name ="flybase" title="When using flybase style" expanded="False">
442 <param name="height_utr" type="float" value="1" min="0" max="1" label="relative height of UTR regions compared to coding regions in flybase style"/>
443 <param name="color_utr" type="color" value="grey" label="Color of UTR regions"/>
444 </section>
445 <section name ="ucsc" title="When using UCSC style" expanded="False">
446 <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/>
447 </section>
448 <section name ="gtf" title="When using gtf as input" expanded="False">
449 <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label"
450 help="Usually transcript_name or gene_name"/>
451 <param name="merge_transcripts" type="boolean" truevalue="true" falsevalue="false" checked="false"
452 label="Merge all transcripts of each gene in a single entry" />
453 </section>
454 </section>
455 </xml>
456 <xml name="lines_macro">
457 <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
458 <param name="line_width" type="float" value="0.5" label="width of line(s)" optional="True"/>
459 <param name="line_style" type="select" label="Style of the line(s)">
460 <option value="solid" selected="True">Solid</option>
461 <option value="dashed">Dashed</option>
462 <option value="dotted">Dotted</option>
463 <option value="dashdot">Dashdot</option>
464 </param>
465 </xml>
466 <xml name="links_color_macro">
467 <conditional name="color_link">
468 <param name="color_link_select" type="select" label="Use color:">
469 <option value="manually" selected="True">manually</option>
470 <option value="colormap">From the 7th field (score)</option>
471 </param>
472 <when value="manually">
473 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
474 </when>
475 <when value="colormap">
476 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
477 <option value="RdYlBu">RdYlBu</option>
478 <option value="Accent">Accent</option>
479 <option value="Spectral">Spectral</option>
480 <option value="Set1">Set1</option>
481 <option value="Set2">Set2</option>
482 <option value="Set3">Set3</option>
483 <option value="Dark2">Dark2</option>
484 <option value="Reds">Reds</option>
485 <option value="Oranges">Oranges</option>
486 <option value="Greens">Greens</option>
487 <option value="Blues">Blues</option>
488 <option value="Greys">Greys</option>
489 <option value="Purples">Purples</option>
490 <option value="Paired">Paired</option>
491 <option value="Pastel1">Pastel1</option>
492 <option value="Pastel2">Pastel2</option>
493 <option value="spring">spring</option>
494 <option value="summer">summer</option>
495 <option value="autumn">autumn</option>
496 <option value="winter">winter</option>
497 <option value="hot">hot</option>
498 <option value="coolwarm">coolwarm</option>
499 <option value="cool">cool</option>
500 <option value="seismic">seismic</option>
501 <option value="terrain">terrain</option>
502 <option value="ocean">ocean</option>
503 <option value="rainbow">rainbow</option>
504 <option value="bone">bone</option>
505 <option value="flag">flag</option>
506 <option value="prism">prism</option>
507 <option value="cubehelix">cubehelix</option>
508 <option value="binary">binary</option>
509 <option value="pink">pink</option>
510 <option value="gray">gray</option>
511 <option value="copper">copper</option>
512 <option value="BrBG">BrBG</option>
513 <option value="BuGn">BuGn</option>
514 <option value="BuPu">BuPu</option>
515 <option value="GnBu">GnBu</option>
516 <option value="OrRd">OrRd</option>
517 <option value="PiYG">PiYG</option>
518 <option value="PRGn">PRGn</option>
519 <option value="PuOr">PuOr</option>
520 <option value="PuRd">PuRd</option>
521 <option value="PuBu">PuBu</option>
522 <option value="RdBu">RdBu</option>
523 <option value="RdGy">RdGy</option>
524 <option value="RdPu">RdPu</option>
525 <option value="YlGn">YlGn</option>
526 <option value="PuBuGn">PuBuGn</option>
527 <option value="RdYlGn">RdYlGn</option>
528 <option value="YlGnBu">YlGnBu</option>
529 <option value="YlOrBr">YlOrBr</option>
530 <option value="YlOrRd">YlOrRd</option>
531 <option value="gist_gray">gist_gray</option>
532 <option value="gist_stern">gist_stern</option>
533 <option value="gist_earth">gist_earth</option>
534 <option value="gist_yarg">gist_yarg</option>
535 <option value="gist_ncar">gist_ncar</option>
536 <option value="gist_rainbow">gist_rainbow</option>
537 <option value="gist_heat">gist_heat</option>
538 <option value="gnuplot">gnuplot</option>
539 <option value="gnuplot2">gnuplot2</option>
540 <option value="CMRmap">CMRmap</option>
541 <option value="bwr">bwr</option>
542 <option value="hsv">hsv</option>
543 <option value="brg">brg</option>
544 <option value="jet">jet</option>
545 <option value="afmhot">afmhot</option>
546 <option value="Accent_r">Accent reversed</option>
547 <option value="Spectral_r">Spectral reversed</option>
548 <option value="Set1_r">Set1 reversed</option>
549 <option value="Set2_r">Set2 reversed</option>
550 <option value="Set3_r">Set3 reversed</option>
551 <option value="Dark2_r">Dark2 reversed</option>
552 <option value="Reds_r">Reds reversed</option>
553 <option value="Oranges_r">Oranges reversed</option>
554 <option value="Greens_r">Greens reversed</option>
555 <option value="Blues_r">Blues reversed</option>
556 <option value="Greys_r">Greys reversed</option>
557 <option value="Purples_r">Purples reversed</option>
558 <option value="Paired_r">Paired reversed</option>
559 <option value="Pastel1_r">Pastel1 reversed</option>
560 <option value="Pastel2_r">Pastel2 reversed</option>
561 <option value="spring_r">spring reversed</option>
562 <option value="summer_r">summer reversed</option>
563 <option value="autumn_r">autumn reversed</option>
564 <option value="winter_r">winter reversed</option>
565 <option value="hot_r">hot reversed</option>
566 <option value="coolwarm_r">coolwarm reversed</option>
567 <option value="cool_r">cool reversed</option>
568 <option value="seismic_r">seismic reversed</option>
569 <option value="terrain_r">terrain reversed</option>
570 <option value="ocean_r">ocean reversed</option>
571 <option value="rainbow_r">rainbow reversed</option>
572 <option value="bone_r">bone reversed</option>
573 <option value="flag_r">flag reversed</option>
574 <option value="prism_r">prism reversed</option>
575 <option value="cubehelix_r">cubehelix reversed</option>
576 <option value="binary_r">binary reversed</option>
577 <option value="pink_r">pink reversed</option>
578 <option value="gray_r">gray reversed</option>
579 <option value="copper_r">copper reversed</option>
580 <option value="BrBG_r">BrBG reversed</option>
581 <option value="BuGn_r">BuGn reversed</option>
582 <option value="BuPu_r">BuPu reversed</option>
583 <option value="GnBu_r">GnBu reversed</option>
584 <option value="OrRd_r">OrRd reversed</option>
585 <option value="PiYG_r">PiYG reversed</option>
586 <option value="PRGn_r">PRGn reversed</option>
587 <option value="PuOr_r">PuOr reversed</option>
588 <option value="PuRd_r">PuRd reversed</option>
589 <option value="PuBu_r">PuBu reversed</option>
590 <option value="RdBu_r">RdBu reversed</option>
591 <option value="RdGy_r">RdGy reversed</option>
592 <option value="RdPu_r">RdPu reversed</option>
593 <option value="YlGn_r">YlGn reversed</option>
594 <option value="PuBuGn_r">PuBuGn reversed</option>
595 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
596 <option value="RdYlGn_r">RdYlGn reversed</option>
597 <option value="YlGnBu_r">YlGnBu reversed</option>
598 <option value="YlOrBr_r">YlOrBr reversed</option>
599 <option value="YlOrRd_r">YlOrRd reversed</option>
600 <option value="gist_gray_r">gist_gray reversed</option>
601 <option value="gist_stern_r">gist_stern reversed</option>
602 <option value="gist_earth_r">gist_earth reversed</option>
603 <option value="gist_yarg_r">gist_yarg reversed</option>
604 <option value="gist_ncar_r">gist_ncar reversed</option>
605 <option value="gist_rainbow_r">gist_rainbow reversed</option>
606 <option value="gist_heat_r">gist_heat reversed</option>
607 <option value="gnuplot_r">gnuplot reversed</option>
608 <option value="gnuplot2_r">gnuplot2 reversed</option>
609 <option value="CMRmap_r">CMRmap reversed</option>
610 <option value="bwr_r">bwr reversed</option>
611 <option value="hsv_r">hsv reversed</option>
612 <option value="brg_r">brg reversed</option>
613 <option value="jet_r">jet reversed</option>
614 <option value="afmhot_r">afmhot reversed</option>
615 </param>
616 </when>
617 </conditional>
618 </xml>
432 </macros> 619 </macros>