Mercurial > repos > bgruening > deeptools_plot_fingerprint
comparison deepTools_macros.xml @ 28:793665fff0f8 draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5
| author | bgruening |
|---|---|
| date | Fri, 19 May 2023 08:34:50 +0000 |
| parents | ca8a7f0ea872 |
| children | b88ebb3672a1 |
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| 27:ca8a7f0ea872 | 28:793665fff0f8 |
|---|---|
| 366 </xml> | 366 </xml> |
| 367 | 367 |
| 368 <xml name="pseudocount"> | 368 <xml name="pseudocount"> |
| 369 <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/> | 369 <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/> |
| 370 </xml> | 370 </xml> |
| 371 | |
| 372 <token name="@REFERENCES@"> | 371 <token name="@REFERENCES@"> |
| 373 | 372 |
| 374 .. class:: infomark | 373 .. class:: infomark |
| 375 | 374 |
| 376 For more information on the tools, please visit our `help site`_. | 375 For more information on the tools, please visit our `help site`_. |
| 481 | 480 |
| 482 | 481 |
| 483 <token name="@multiple_input_bams@"> | 482 <token name="@multiple_input_bams@"> |
| 484 <![CDATA[ | 483 <![CDATA[ |
| 485 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": | 484 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": |
| 486 #set custom_labels=labels | 485 #set custom_labels=$custom_sample_labels_conditional.labels |
| 487 #end if | 486 #end if |
| 488 #set files=[] | 487 #set files=[] |
| 489 #set labels=[] | 488 #set labels=[] |
| 490 #import re | 489 #import re |
| 491 #if $multibam_conditional.orderMatters == "No": | 490 #if $multibam_conditional.orderMatters == "No": |
| 496 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' && | 495 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' && |
| 497 #else: | 496 #else: |
| 498 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' && | 497 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' && |
| 499 #end if | 498 #end if |
| 500 #silent $files.append("'%s.bam'" % $counter) | 499 #silent $files.append("'%s.bam'" % $counter) |
| 501 #silent $labels.append("'%s'" % identifier) | 500 #silent $labels.append("'%s'" % $identifier) |
| 502 #end for | 501 #end for |
| 503 #else: | 502 #else: |
| 504 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): | 503 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): |
| 505 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier)) | 504 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier)) |
| 506 ln -s '${f.bamfiles}' './${counter}.bam' && | 505 ln -s '${f.bamfiles}' './${counter}.bam' && |
| 520 </token> | 519 </token> |
| 521 | 520 |
| 522 <token name="@multiple_input_bigwigs@"> | 521 <token name="@multiple_input_bigwigs@"> |
| 523 <![CDATA[ | 522 <![CDATA[ |
| 524 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": | 523 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": |
| 525 #set custom_labels=labels | 524 #set custom_labels=$custom_sample_labels_conditional.labels |
| 526 #end if | 525 #end if |
| 527 #set files=[] | 526 #set files=[] |
| 528 #set labels=[] | 527 #set labels=[] |
| 529 #import re | 528 #import re |
| 530 #if $multibigwig_conditional.orderMatters == "No": | 529 #if $multibigwig_conditional.orderMatters == "No": |