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comparison hal_halStats.xml @ 1:4b1c38d744a0 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 30ac0af6dfa729277011bcd73cd5560efa03fb97
author iuc
date Wed, 18 Mar 2026 15:06:06 +0000
parents 25dcde5bf94e
children
comparison
equal deleted inserted replaced
0:25dcde5bf94e 1:4b1c38d744a0
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 set -o pipefail; ## Sets the pipeline’s exit code to halStats’s on failure. 9 set -o pipefail; ## Sets the pipeline’s exit code to halStats’s on failure.
10 ( ## echo headers for specific numerical data 10 ## echo headers for specific numerical data
11 #if $mode.option == '--baseComp': 11 #if $mode.option == '--baseComp':
12 echo -e 'fraction_of_As\tfraction_of_Gs\tfraction_of_Cs\tfraction_of_Ts'; 12 echo -e 'fraction_of_As\tfraction_of_Gs\tfraction_of_Cs\tfraction_of_Ts' >> '$out_file' &&
13 #else if $mode.option == '--numSegments': 13 #else if $mode.option == '--numSegments':
14 echo -e 'numTopSegments\tnumBottomSegments'; 14 echo -e 'numTopSegments\tnumBottomSegments' >> '$out_file' &&
15 #end if 15 #end if
16 halStats 16 halStats
17 #if $mode.option == '--allCoverage': 17 #if $mode.option == '--allCoverage':
18 --allCoverage 18 --allCoverage
19 #else if $mode.option == '--branches': 19 #else if $mode.option == '--branches':
24 --metaData 24 --metaData
25 #else if $mode.option == '--root': 25 #else if $mode.option == '--root':
26 --root 26 --root
27 #else if $mode.option == '--tree': 27 #else if $mode.option == '--tree':
28 --tree 28 --tree
29 #else if $mode.option == '--assembly':
30 --assembly
29 #else if $mode.option == '--baseComp': 31 #else if $mode.option == '--baseComp':
30 --baseComp '$mode.baseComp' 32 --baseComp '$mode.baseComp'
31 #else if $mode.option == '--bedSequences': 33 #else if $mode.option == '--bedSequences':
32 --bedSequences '$mode.bedSequences' 34 --bedSequences '$mode.bedSequences'
33 #else if $mode.option == '--bottomSegments': 35 #else if $mode.option == '--bottomSegments':
58 --spanRoot '$mode.spanRoot' 60 --spanRoot '$mode.spanRoot'
59 #else if $mode.option == '--topSegments': 61 #else if $mode.option == '--topSegments':
60 --topSegments '$mode.topSegments' 62 --topSegments '$mode.topSegments'
61 #end if 63 #end if
62 '$input_hal' 64 '$input_hal'
63 ## Pipes specific output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree. 65 ## Pipes specific output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
64 #if $mode.option == '--allCoverage' or $mode.option == '--sequenceStats' or $mode.option == '--percentID' or $mode.option == '--coverage': 66 #if $mode.option == '--allCoverage' or $mode.option == '--sequenceStats' or $mode.option == '--percentID' or $mode.option == '--coverage' or $mode.option == '--assembly':
65 | tr ',' '\t' 67 | sed $'s/, */\t/g'
66 #else if $mode.option == '--numSegments': 68 #else if $mode.option == '--numSegments':
67 | tr ' ' '\t' ## Replace spaces 69 | tr ' ' '\t' ## Replace spaces
68 #end if 70 #end if
69 ) > '$out_file' 71 >> '$out_file'
70 ]]></command> 72 ]]></command>
71 <inputs> 73 <inputs>
72 <expand macro="input_hal"/> 74 <expand macro="input_hal"/>
73 <conditional name="mode"> 75 <conditional name="mode">
74 <param name="option" type="select" label="Select the type of statistics you are interested in"> 76 <param name="option" type="select" label="Select the type of statistics you are interested in">
76 <option value="--genomes">List of genomes in alignment (--genomes)</option> 78 <option value="--genomes">List of genomes in alignment (--genomes)</option>
77 <option value="--sequences">List of sequences in a given genome (--sequences)</option> 79 <option value="--sequences">List of sequences in a given genome (--sequences)</option>
78 <option value="--bedSequences">List of sequences in a given genome (in BED format) (--bedSequences)</option> 80 <option value="--bedSequences">List of sequences in a given genome (in BED format) (--bedSequences)</option>
79 <option value="--sequenceStats">Stats for each sequence in a given genome (--sequenceStats)</option> 81 <option value="--sequenceStats">Stats for each sequence in a given genome (--sequenceStats)</option>
80 <option value="--tree">Newick tree (--tree)</option> 82 <option value="--tree">Newick tree (--tree)</option>
83 <option value="--assembly">Assembly stats for each genome (--assembly)</option>
81 <option value="--branches">List of branches specified by the child genome (--branches)</option> 84 <option value="--branches">List of branches specified by the child genome (--branches)</option>
82 <option value="--span">Branches on path (or spanning tree) between given list of genomes (--span)</option> 85 <option value="--span">Branches on path (or spanning tree) between given list of genomes (--span)</option>
83 <option value="--spanRoot">Genomes on path (or spanning tree) with spanning tree root between given list of genomes (--spanRoot)</option> 86 <option value="--spanRoot">Genomes on path (or spanning tree) with spanning tree root between given list of genomes (--spanRoot)</option>
84 <option value="--children">Names of children of a given genome (--children)</option> 87 <option value="--children">Names of children of a given genome (--children)</option>
85 <option value="--root">Root genome name (--root)</option> 88 <option value="--root">Root genome name (--root)</option>
172 <expand macro="sanitizer_default"/> 175 <expand macro="sanitizer_default"/>
173 <expand macro="validator_trim"/> 176 <expand macro="validator_trim"/>
174 </param> 177 </param>
175 </when> 178 </when>
176 <when value="--root"/> 179 <when value="--root"/>
180 <when value="--assembly"/>
177 <when value="--sequenceStats"> 181 <when value="--sequenceStats">
178 <param name="sequenceStats" type="text" value="" label="Genome name"> 182 <param name="sequenceStats" type="text" value="" label="Genome name">
179 <expand macro="sanitizer_default"/> 183 <expand macro="sanitizer_default"/>
180 <expand macro="validator_trim"/> 184 <expand macro="validator_trim"/>
181 </param> 185 </param>
211 <when input="mode.option" value="--coverage" format="tabular"/> 215 <when input="mode.option" value="--coverage" format="tabular"/>
212 <when input="mode.option" value="--chromSizes" format="tabular"/> 216 <when input="mode.option" value="--chromSizes" format="tabular"/>
213 <when input="mode.option" value="--baseComp" format="tabular"/> 217 <when input="mode.option" value="--baseComp" format="tabular"/>
214 <when input="mode.option" value="--metaData" format="tabular"/> 218 <when input="mode.option" value="--metaData" format="tabular"/>
215 <when input="mode.option" value="--genomeMetaData" format="tabular"/> 219 <when input="mode.option" value="--genomeMetaData" format="tabular"/>
220 <when input="mode.option" value="--assembly" format="tabular"/>
216 <when input="mode.option" value="--bedSequences" format="bed"/> 221 <when input="mode.option" value="--bedSequences" format="bed"/>
217 <when input="mode.option" value="--topSegments" format="bed"/> 222 <when input="mode.option" value="--topSegments" format="bed"/>
218 <when input="mode.option" value="--bottomSegments" format="bed"/> 223 <when input="mode.option" value="--bottomSegments" format="bed"/>
219 </change_format> 224 </change_format>
220 </data> 225 </data>
236 <conditional name="mode"> 241 <conditional name="mode">
237 <param name="option" value="--allCoverage"/> 242 <param name="option" value="--allCoverage"/>
238 </conditional> 243 </conditional>
239 <output name="out_file" ftype="tabular"> 244 <output name="out_file" ftype="tabular">
240 <assert_contents> 245 <assert_contents>
241 <has_line line="FromGenome&#009; ToGenome&#009; sitesCovered1Times&#009; sitesCovered2Times&#009; sitesCovered3Times&#009; sitesCovered4Times&#009; sitesCovered5Times"/> 246 <has_line line="FromGenome&#009;ToGenome&#009;sitesCovered1Times&#009;sitesCovered2Times&#009;sitesCovered3Times&#009;sitesCovered4Times&#009;sitesCovered5Times"/>
242 <has_line line="Genome_1&#009; Genome_1&#009; 5472&#009; 4688&#009; 3516&#009; 2637&#009; 1465"/> 247 <has_line line="Genome_1&#009;Genome_1&#009;5472&#009;4688&#009;3516&#009;2637&#009;1465"/>
243 <has_n_lines n="10"/> 248 <has_n_lines n="10"/>
249 </assert_contents>
250 </output>
251 </test>
252 <test expect_num_outputs="1">
253 <param name="input_hal" value="halTest.hal"/>
254 <conditional name="mode">
255 <param name="option" value="--coverage"/>
256 <param name="coverage" value="Genome_1"/>
257 </conditional>
258 <output name="out_file" ftype="tabular">
259 <assert_contents>
260 <has_line line="Genome&#009;sitesCovered1Times&#009;sitesCovered2Times&#009;sitesCovered3Times&#009;sitesCovered4Times&#009;sitesCovered5Times"/>
261 <has_line line="Genome_1&#009;5472&#009;4688&#009;3516&#009;2637&#009;1465"/>
262 <has_n_lines n="4"/>
244 </assert_contents> 263 </assert_contents>
245 </output> 264 </output>
246 </test> 265 </test>
247 <test expect_num_outputs="1"> 266 <test expect_num_outputs="1">
248 <param name="input_hal" value="halTest.hal"/> 267 <param name="input_hal" value="halTest.hal"/>
331 <param name="option" value="--sequenceStats"/> 350 <param name="option" value="--sequenceStats"/>
332 <param name="sequenceStats" value="Genome_0"/> 351 <param name="sequenceStats" value="Genome_0"/>
333 </conditional> 352 </conditional>
334 <output name="out_file" ftype="tabular"> 353 <output name="out_file" ftype="tabular">
335 <assert_contents> 354 <assert_contents>
336 <has_line line="SequenceName&#009; Length&#009; NumTopSegments&#009; NumBottomSegments"/> 355 <has_line line="SequenceName&#009;Length&#009;NumTopSegments&#009;NumBottomSegments"/>
337 <has_line line="Genome_0_seq&#009; 1758&#009; 0&#009; 8"/> 356 <has_line line="Genome_0_seq&#009;1758&#009;0&#009;8"/>
338 <has_n_lines n="3"/> 357 <has_n_lines n="3"/>
339 </assert_contents> 358 </assert_contents>
340 </output> 359 </output>
341 </test> 360 </test>
342 <test expect_num_outputs="1"> 361 <test expect_num_outputs="1">
370 <param name="option" value="--percentID"/> 389 <param name="option" value="--percentID"/>
371 <param name="percentID" value="Genome_0"/> 390 <param name="percentID" value="Genome_0"/>
372 </conditional> 391 </conditional>
373 <output name="out_file" ftype="tabular"> 392 <output name="out_file" ftype="tabular">
374 <assert_contents> 393 <assert_contents>
375 <has_line line="Genome&#009; % ID&#009; numID&#009; numSites"/> 394 <has_line line="Genome&#009;% ID&#009;numID&#009;numSites"/>
376 <has_line line="Genome_0&#009; 1&#009; 1758&#009; 1758"/> 395 <has_line line="Genome_0&#009;1&#009;1758&#009;1758"/>
377 <has_n_lines n="5"/> 396 <has_n_lines n="5"/>
378 </assert_contents> 397 </assert_contents>
379 </output> 398 </output>
380 </test> 399 </test>
381 <test expect_num_outputs="1"> 400 <test expect_num_outputs="1">
464 <output name="out_file" ftype="tabular"> 483 <output name="out_file" ftype="tabular">
465 <assert_contents> 484 <assert_contents>
466 <has_line line="fraction_of_As&#009;fraction_of_Gs&#009;fraction_of_Cs&#009;fraction_of_Ts"/> 485 <has_line line="fraction_of_As&#009;fraction_of_Gs&#009;fraction_of_Cs&#009;fraction_of_Ts"/>
467 <has_line line="0.5&#009;0&#009;0.5&#009;0"/> 486 <has_line line="0.5&#009;0&#009;0.5&#009;0"/>
468 <has_n_lines n="2"/> 487 <has_n_lines n="2"/>
488 </assert_contents>
489 </output>
490 </test>
491 <test expect_num_outputs="1">
492 <param name="input_hal" value="halTestExtended.hal"/>
493 <conditional name="mode">
494 <param name="option" value="--span"/>
495 <param name="span" value="Genome_0,Genome_2"/>
496 </conditional>
497 <output name="out_file" ftype="txt">
498 <assert_contents>
499 <has_text text="Insert Genome_2"/>
500 <has_n_lines n="1"/>
501 </assert_contents>
502 </output>
503 </test>
504 <test expect_num_outputs="1">
505 <param name="input_hal" value="halTest.hal"/>
506 <conditional name="mode">
507 <param name="option" value="--assembly"/>
508 </conditional>
509 <output name="out_file" ftype="tabular">
510 <assert_contents>
511 <has_line line="Genome&#009;TotalLength&#009;NumContigs&#009;MinContigLength&#009;MaxContigLength&#009;MeanContigLength&#009;MedianContigLength&#009;N50&#009;L50"/>
512 <has_line line="Genome_1&#009;5472&#009;1&#009;5472&#009;5472&#009;5472&#009;0&#009;5472&#009;1"/>
513 <has_n_lines n="5"/>
469 </assert_contents> 514 </assert_contents>
470 </output> 515 </output>
471 </test> 516 </test>
472 </tests> 517 </tests>
473 <help><![CDATA[ 518 <help><![CDATA[
480 525
481 **Output** 526 **Output**
482 527
483 The tool generates different output formats based on the selected type of statistic: 528 The tool generates different output formats based on the selected type of statistic:
484 529
485 - **Tabular** for --coverage, --allCoverage, --sequenceStats, --percentID, --baseComp, --chromSizes, --metaData, --numSegments, or --genomeMetaData 530 - **Tabular** for --coverage, --allCoverage, --sequenceStats, --percentID, --baseComp, --chromSizes, --metaData, --numSegments, --genomeMetaData, or --assembly
486 - **BED** for --bedSequences, --topSegments, or --bottomSegments 531 - **BED** for --bedSequences, --topSegments, or --bottomSegments
487 - Plain **text** for all other type of statistics 532 - Plain **text** for all other type of statistics
488 533
489 ]]></help> 534 ]]></help>
490 <expand macro="citation"/> 535 <expand macro="citation"/>